DNA Condensed Phase and DNA-Inorganic Hybrid Mesostructured

Chapter 4

DNA Condensed Phase and DNA-Inorganic Hybrid Mesostructured Materials Downloaded by UNIV OF FLORIDA on October 26, 2017 | http://pubs.acs.org Publication Date (Web): October 25, 2017 | doi: 10.1021/bk-2017-1252.ch004

Yuanyuan Cao and Shunai Che* School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China *E-mail:[email protected]

The compaction and decompaction processes of DNA compose the crucial part in cell life cycle. The research on those compacted phases of DNA derives from both biology and soft matter science, which promotes the development of nucleic acid research and modern nanotechnology, further brings real benefits for human such as the improving of gene therapy. In this chapter, we have first introduced the organic soft matter that originates from the self-assembly of DNA superstructures, as well as several kinds of methods for inducing condensed phase of DNA. Then we have focused on the DNA templated mesostructured assemblies for guiding the formation of inorganic mesoporous materials. The fabrication of those materials main achieved through self-assembly process combining the artificial biomineralization methods, which will promote the designing of novel optical or electric materials.

The “soft matter” field, which mainly concerns polymers, colloids, surfactants, liquid crystals, biomolecules and molecular assemblies, is an exciting and fast-developing field. It is an interdisciplinary subject that utilizes aspects of physics, chemistry and materials science as well as biochemistry or engineering in specific cases. Soft matter has typically been distinguished from traditional “hard materials” through differences between their macroscopic mechanism properties. However, today, the classification is not simply restricted to macroscopic properties but is also considered from a kinetic energy viewpoint regarding the © 2017 American Chemical Society Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

Downloaded by UNIV OF FLORIDA on October 26, 2017 | http://pubs.acs.org Publication Date (Web): October 25, 2017 | doi: 10.1021/bk-2017-1252.ch004

intermolecular interactions and arrangements of the components, in which the ordering is generally intermediate between that of a crystalline solid and a liquid. Owing to recent developments in the soft matter field and biology, biological soft materials, which have existed in nature over billions of years, have rapidly gained more attention than ever before. Although biological soft matter systems appear more complex than artificial material systems, concepts from polymer physics, physical chemistry and colloidal science as well as surface chemistry have yielded great insights into organism formation mechanisms, such as fibril building, protein crystallization or membrane fluidity. In turn, the concepts from nature have also inspired rapid developments in soft materials, examples include constructing complex structures from assemblies of biopolymers or exploiting nanotechnology to make devices based on the self-organization of polymers (1). Biology related soft matter research has mainly focused on studying comprehensive living systems and the cross-interactions between the different kinds of components, such as proteins, nucleic acids, polysaccharides and lipids, within them. The basic role of DNA, or deoxyribonucleic acid, is to store huge amounts of genetic code and to provide the blueprint for the machinery of life: proteins. When DNA replicates itself, sophisticated information transcription and compaction/decompaction processes occur that are highly efficient and fast and involve cooperative interactions with other biological counterparts that are still not completely understood. The compaction process of DNA in vitro and in vivo can be considered as a process that exists at the cross section between soft matter science and biology, which can promote both the development of nucleic acid research and modern nanotechnology. For instance, the recently popular concept of gene therapy offers a fundamental approach for treating inherited or acquired diseases, which requires introducing specifically engineered genes into a patient’s cells to act as a drug. This technology requires a deep understanding of how to collapse extended DNA chains into compact, orderly particles or to package DNA into vectors for delivery, which can enter the target cell and quickly decompose (2, 3). All of these processes demand understanding the condensed structures of DNA. However, since studying the behavior of DNA in vivo needs rather complex observation methods, research on DNA condensation in vitro using an artificial system is considered to be a smart and reliable substitute. In this chapter, instead of discussing single molecular conformations at the atomistic level, we introduced ordered soft matter that originates from the self-assembly of DNA superstructures and aggregates, and we especially mentioned its chiral features, which are a vital part of DNA. Then, starting from materials science, we will mainly introduce how the DNA mesostructured assemblies work as templates for guiding the formation of inorganic materials through the biomineralization process.

1. Short Introduction of DNA DNA is a typical chain-like polymer composed of polymerized nucleotide monomers. It is composed of two polyester chains made up of alternating sugar 50 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


(D-2-deoxyribose) and phosphate groups. Each sugar group is attached to four different kinds of nitric bases, two major purine bases (adenine (A) and guanine (G)) and two major pyrimidine bases (cytosine (C) and thymine (T)), which code genetic information through an infinite number of different permutations. Hydrogen bonds between the specifically paired pyrimidines and purines (called base pairs) connect and stabilize the two spiral chains, causing them to twist into a double helix to form the three-dimensional secondary structure of DNA. The typical, well-known, B-conformation DNA, which was discovered in 1953 by Watson and Crick (4), is a right-handed double helix with a diameter of 2.2 nm and an approximately 3.4 nm helical pitch composed of 10 base pairs; a schematic of the double helix is shown in Figure 1 (5). Although the B-type secondary structure is the most stable conformation under physiological conditions, it is not the constant conformation of DNA. The conformation changes from the B-type to the right-handed duplex A-type or the left-handed duplex Z-type depending on variations in the external solution environment, such as the ionic strength, solvent and temperature (6, 7), or the base pair sequences (8).

Figure 1. The structural parameters of the B-type DNA double helix in solution. An important aspect that should be considered when studying the behavior of DNA in solution is its intrinsic polyelectrolyte qualities. The peripheral phosphate groups on the polyester chains endow the backbone with two negative charges per base pair. The pKa of the phosphate groups of DNA is approximately 1; thus, the backbone can be fully charged at pH 7 (However, the phosphomonoester groups on the ends of the chain have a second pKa value of approximately 6) (9). The charges on biomolecules have great physiological significance. They can prevent homologous intermolecular interactions by electrostatic repulsion and form desired complexes with oppositely charged molecules. For example, electrostatic interactions are mainly attributed to the formation the nucleosomes when DNA wraps around histone. The formation of this kind of complex is also affected by the chain flexibility of the DNA molecules. The flexibility parameter that describes the ability of linear 51 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


molecules to bend locally is the persistence length, which is also known as the orientational correlation length. The persistence length of DNA is approximately 50 nm, as measured from various methods, and depends on the salt concentration in the range of 1-2 mM NaCl (10–12). The flexibility of DNA dramatically changes when its length reaches this threshold value. When DNA is shorter than the persistence length, it is rather stiff and rodlike, while it will behave as a wormlike chain when the length reaches a few persistence lengths. Additionally, the packing of DNA inside a viral capsid is affected by the persistence length.

2. The Mesostructured Packing Phase of DNA 2.1. DNA Assemblies Because DNA plays the role of a carrier for a huge amount of genetic information in a very limited space within a cell, the in vivo packing of DNA, which may be several meters long, is usually very tight. Except for the highly hierarchical DNA storage chromatin in eukaryotic cell nuclei, in most extrachromosomal organisms, such as in sperm heads, virus capsids, and bacterial nucleoids, the volume concentrations of DNA can reach 70% W/V in cells (13–15). The packing is highly efficient and dense but remains accessible for transcription or replication; thus, DNA undergoes alternative condensation and decondensation processes during the cell cycle. The efficient packing ordering requirements and the need for the fluid structure to remain accessible require DNA to under liquid crystal-like organization (16). The formation mechanisms of the liquid-crystalline phases of concentrated solutions of DNA may be related to the tendency of semi-rigid polymers to form liquid-crystalline phases during concentration processes. In 1961, Robinson first reported on the possible liquid crystal phase of DNA in vitro as a supplemental study that was adjunct to a phase study on the liquid crystal behavior of PBLG (poly-γ-benzyl-L-glutamate) and suspected that the phase was of the cholesteric type (17, 18). Later, short DNA fragments with lengths corresponding to the persistence length were applied to study multiple liquid-crystalline phases, as these rigid fragments rule out the entanglement problems that within long DNA molecules (19). Simply by increasing the concentration, isotropic DNA can form multiple liquid-crystalline phases from chiral liquid phases, such as the blue phase (also studied as the precholesteric phase) and the cholesteric phase, to achiral liquid-crystalline phases, such as the 2D columnar hexagonal phase, then to true crystals, such as the 3D hexagonal and 3D orthorhombic phases. The schematic models of these phases are shown in Figure 2 (20, 21). Although it is difficult to obtain well-organized liquid-crystalline phases using long DNA, it appears that the polymer length does not alter the nature of the liquid-crystalline phases, which means that these phases may also appear with long DNA but require time to organize and stabilize. However, the length of the polymer can affect the defects and phase transitions. 52 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 2. Schematic representation of the structures of multiple liquid-crystals: (A) Blue phase building blocks with a right-handed double-twist cylinder; (B) Right-handed chiral cholesteric phase; (C) 2D columnar hexagonal structure; (D) 3D hexagonal structure; and (E) 3D orthorhombic phase. Reproduced with permission (21). Copyright 2015, Wiley-VCH Verlag GmbH & Co. KGaA.

The surface charge of DNA strongly contributes to the attraction between these rod-like polyelectrolytes. Kornyshev et al. (22) developed an “electrostatic zipper” model to explain the dense packing and counterion specificity of DNA condensation. Strips composed of positively charged counterions adsorbed in the grooves and negatively charged lines of the phosphates allowed oppositely charged groups to approach to form DNA-DNA contacts, creating a “zipper” that pulls the molecules through electrostatic interactions and fastens the molecules together. The zipper interaction model has given rise to a special packing phase, the 2D square phase, which is rarely found naturally (23). The 2D square phase appears in a narrow concentration range and has a loose packing arrangement with a d-spacing ratio of √2/1, which is different from the spatial confinement packing of noncharged rods. This special mesostructure occurs under subtle charge balance conditions, which we will discuss in detail in the following section. 2.2. Chiral DNA Assemblies 2.2.1. The Cholesteric and Blue Phase The chirality of DNA affects not only the secondary double helix structure but also the packed tertiary structure. Considering the geometry of DNA, the helical shapes affect the packing behavior of rodlike DNA under confinement conditions. Two helices usually prefer to align at an angle instead of parallel to each other because the helices fit well into each other’s grooves. When DNA is not present at a very high concentration, the formation of cholesteric (single-twist plywood) and blue phases (double-twist cylinders) originates from spontaneous twisting. Right-handed B-DNA usually forms the left-handed cholesteric phase in the absence of other disturbances. This is the case for long DNA molecules; however, for ultrashort DNA in the range of 8-20 bp, spontaneous right-handed chiral phases can be obtained (24). In the cholesteric phase, DNA molecules are aligned in parallel, and their orientation rotates continuously along a direction that is perpendicular to the helical axis of the stacking layers. The helical pitch usual varies from 1.5 to 3.5 μm (25). One should notice that the phase is continuous, and the term “layer” is not a real plane but is simply used to clarify the stacking. 53 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Although the steric interactions between the chiral shapes favor the formation of the right-hand cholesteric phase, the strong repulsion interactions from the helical-distributed electrostatic charges on the surface of the DNA induce a chirality inversion into a left-handed structure. Thus, extrinsic factors that affect the geometrical parameters and electronic charges of DNA, such as groove binders, intercalators or polycations, greatly affect the cholesteric pitch (26). Even the sign of the cholesteric phase can be changed by adding divalent cations, such as the right-handedness that is induced by the presence of Mg2+ and Ca2+ (27, 28). In higher DNA concentrations, DNA forms either 2D or 3D hexagonal phases. Dense packing prevents spontaneous twisting between the molecules, and the resulting structures originate from the competition between the chiral order and dense packing constraints (29). Within a special given concentration range, the chiral cholesteric and achiral hexagonal phases may coexist because of phase transitions in which slight untwisting occurs in the cholesteric structure. The two-fold symmetry axes of the hexagonal phase become parallel to the helical axes of the cholesteric phase. During the transition from the isotropic phase to the cholesteric phase of DNA, the blue phase has been observed within a narrow concentration range. In this phase, the DNA molecules assume a double-twist structure within small cylindrical domains that are 40-200 nm wide and 800 nm long (30). The helical pitch length in the blue phase, which was calculated as 800 nm, is much smaller than that of the cholesteric phase. The double-twist cylinders can further densely assemble into a long-range BP I phase with body-centered cubic symmetry or a loose random BP III phase.

2.2.2. Circular Dichroism (CD) of Chiral DNA Aggregation An important feature of the chiral condensed phase of DNA is the presence of anomalous circular dichroism (CD) signals, which are tens to thousands of times higher than those of dispersed DNA molecules. The spectrum obtained within the absorption band of DNA is called psi (polymer-and-salt-induced, also written as ψ)-type CD. These signals are produced because of induced oscillating dipole moments that are coupled over all of the particles and the generation of collective excitation modes, which are the eigenmodes of the particle in which the shape depends on the long-range internal organization within the particles (31). In this situation, long-range chirality permits “spatial-resonance” between the appropriate handed circular polarization with very efficient energy exchange, inducing extremely strong circular dichroism signals. In addition, the shape of the spectrum usually has long tails outside the usual absorption band of DNA that extend toward the red wavelengths because of the preferential scattering effect of the long-range chiral aggregates from one circular polarized light (14). Typical CD spectra comparing individual B-DNA prior to and after condensation is shown in Figure 3 (32).

54 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 3. CD spectra of B-DNA prior to and after condensation with PEG. Reproduced with permission (32). Copyright, 1991, American Chemical Society.

3. Organic DNA Assemblies There are multiple ordered condensed phases of DNA, that behave as large-scale mesophases or 3D crystals with distinct morphologies. Compaction can occur either as a result of intermolecular aggregation or as a result of self-condensation or intramolecular aggregation of a single DNA molecule. In solution, these phases can be obtained using various types of methods: a) DNA can be confined into a restricted volume by preparing concentrated water solutions of DNA in the presence of monovalent ions and controlling the concentration by the adjusting the amount of added water. b) DNA can interact with multivalent counterions, such as polyamines, cationic polypeptides polylysine or histone H1, biologically derived liposomes or cationic lipids. c) DNA can be condensed by applying osmotic pressure or through the presence of a dehydrating agent, such as a neutral polymer (polyethylene glycol (PEG)) or ethanol. These condensates generally have orderly, toroidal or rodlike shapes and sizes similar to those of DNA that is gently lysed from phase heads. According to the aggregation process, the resulting structures have been referred to as polymer-and-salt-induced DNA (ψ-DNA), which we introduced before. The in vitro condensation of DNA is both biologically and physically interesting. This process can be regarded as a model for DNA packing within intracellular structures from a biological viewpoint and a typical example of a polymer self-assembly process from a physical viewpoint (33). In addition, the in vitro condensation of DNA inspires gene therapy as an alternative to using recombinant virus vectors and provides new structures for materials design.



3.1. DNA Condensation and the Theory of Counterion Condensation Since DNA can be regarded as a polyelectrolyte with a charge density of 1 e/1.7 Å (2), DNA condensation prefers to the electrostatic attraction between the negatively charged phosphate groups of the outer polyester chains of DNA with a cationic species. A fraction of counterions is bound to the DNA chains because of strong electrostatic attraction and reduces the electrostatic repulsion between the polyelectrolyte chains, which means that the effective charge becomes smaller than that calculated using stoichiometry. This phenomenon is called counterion condensation (also known as Manning condensation). The Manning theory has been found to be consistent with experiments in that it predicts the approximate constant value of the degree of neutralization required to collapse DNA for various ionic conditions. According to the Manning model, the charge density parameter ξ of DNA is 4.2, and the fraction of charges neutralized can be simply expressed as:

which reveals that, on average, three quarters of the bases are neutralized when condensation occurs. Wilson and Bloomfield developed the Manning theory to determine the extent of DNA charge neutralization using multivalent cations and found that the collapse of DNA occurred at ~89% phosphate charge neutralization using polyamines in aqueous solutions. When the charges become neutralized and counterions are released, the DNA chains begin to partially collapse (1).

3.2. DNA-Polyamine Complex The condensation or aggregation of DNA is a continuous cycle for vital cellular processes and has acquired considerable importance in recent years as a model system to analyze DNA-related metabolism and to promote research on gene uptake by cells for gene therapy. The terms condensation and aggregation describe similar phenomena but have a few differences. Condensation is the formation of individual discrete particles with a distinct morphology, and aggregation is the formation of larger and possibly more amorphous accumulations of molecules (33). According to the theory mentioned above, it is clear that one approach to induce the condensation and aggregation of DNA is to screen negative charges with the phosphate groups of DNA by adding multivalent cations, such as naturally occurring polyamines, cationic polypeptides, proteins (such as histone), inorganic metal salts Co(NH3)63+, polyamino lipids and cationic lipids (34–39). 56 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


3.2.1. Condensation by Polyamines Polyamines are ubiquitous components of cells and are involved in many fundamental biological processes in organisms, such as cell growth and differentiation (40, 41). These aliphatic polycationic compounds possess multiple positive charges at physiological pH levels because of the protonation of their amine groups, which endows them with a high affinity for the acidic constituents of cells, such as nucleic acids, acidic proteins, phospholipids and ATP (35). Naturally extracted spermidine (3+), spermine (4+) and diamine putrescine are the most commonly used polyamines for compressing DNA (Although from the concepts of polymer science, it is more accurate to refer to them as oligoamines). They bind to the phosphate groups of DNA and reduce the repulsion interactions to induce the collapse (occurring in single DNA molecule) or aggregation (occurring between more than one DNA molecule) of long DNA molecules in the form of rods or toroids. The toroids formed from the collapse of isolated long DNA chains exhibit local hexagonal packing (Figure 4A) (42). For the short DNA fragments with a 146 bp length (within the persistence length range), the aggregates are not restricted to microscopic domains, extend over long-range distances and are liquid crystalline in the cholesteric or hexagonal phase (43). However, the addition of polyamine cations to DNA solutions first precipitates the DNA, but a further addition resolubilizes the DNA aggregates (44). Livolan et al. (45) determined the concentration thresholds between DNA and polyamine for DNA precipitation and resolubilization, using the “ion-bridging” model based on electrostatic bridging. Furthermore, phase diagrams (35, 46) have been developed to clarify these processes, in which three regimes of DNA concentrations are identified (a schematic representation is shown in Figure 4B). Other factors that influence the condensation process are the properties of the amino species. Thomas et al. (47) tested DNA precipitation/resolubilization phenomena using various kinds of natural and synthetic polyamines. Both the increasing of cations and the variation of structure, especially substituting polyamine, would exert remarkable effects on the precipitate and the of polyamines to resolubilize the DNA. PEI (polyethylenimine) is another kind of the classic counterion polymer that is commonly applied for nonviral gene delivery (48). It is a water soluble polymer with highly positive charges, and every third atom nitrogen can be protonated in a broad range of pH values. Both branched and linear PEI can provide strong electrostatic interactions that lead to the partial condensation of the normally large hydrodynamic volume of DNA and are supposed to be among the most transfection efficient nonviral vectors in vitro and in vivo. The intrinsic properties of PEI, such as its molecular weight and conformation, affect the properties of the formed DNA/PEI complexes and the subsequent cell delivery efficiency. When the metal ions are introduced into the polymer system, the produced polymeric metal complexes are effective to promote the DNA condensation and increase the gene transfection efficiency (49). The polymeric metal complexs synthesized from Fe3+ ions or Zn2+ ions chelating with PEI or imidazole group containing polymers show a improvement of the condensation and transfection efficiency (50, 51). 57 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 4. (A) Cryo-electron micrograph of λDNA toroids with DNA fringes visible around nearly the entire circumference of the toroid and simulated TEM images of a model toroid constructed from a single continuous path. (B) Schematic representation of the phase diagram for the precipitation of DNA fragments in the presence of spermine. The precipitation domain, in which the dense precipitate separates from the dilute supernatant, is limited by the Cprecip and Credissol curves. In this representation, each experimental point is defined by the DNA concentration (CDNA phosphate) and the spermine salt concentration (Cspermine). Reproduced with permission (35, 42). Copyright 2001 National Academy of Sciences. 2005, the Biophysical Society.

3.2.2. DNA “Beads-on-String” Nucleosome-like Structure In somatic eukaryotic cells, DNA is associated with cationic histone proteins to form the highly periodic structures of nucleosomes. Nucleosomes consists of 147 bp DNA wrapped around a 7 nm cationic octamer of histone proteins, which further hierarchically assemble into chromatin fibers that are confined in a limited volume. Those complex structures are still a matter of debate, and many articles have reported the exploration of their structures using microscopy methods (52–54). Another approach to study the compaction of genomic DNA 58 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


in chromatin is to artificially wrap DNA around charged hard spheres to yield the so-called “beads-on-string” structures found in chromatin, to investigate the detailed structure and formation mechanisms using an analogous system. Since histone octamers are disc-shaped nanostructures with positively charged binding sites, polymers that have charged hard spherical cores have been considered as protein substitutes. Chen et al. (55–57) have used polyamidoamine (PAMAM) dendrimers to mimic histone proteins. The complexes of DNA with the dendrimers exhibited three distinct nanostructures characterized by different degrees of DNA bending (Figure 5A), which were revealed using synchrotron small angle X-ray scattering (SAXS). When the dendrimers were highly protonated, “chromatin-like fibers” composed of “nucleosome-like” units were formed (Figure 5Aa3). A further higher-ordered assembled “beads-on-string” structure was achieved using block-copolymer polyethylene glycol-b-poly-4-vinylpyridine (PEG-b-PVP) micelles with an inert shell and a positively charged core (58). The micelles preorganized in the “beads-on-string” structure and further self-assembled along the strings into core-shell structured solenoidal nanofibers (Figure 5B). The two-stage assembly process of the DNA/micelles was a high fidelity mimic of the complex assembly mode of chromatin, proving that the synthetic macromolecule was very effective for mimicking the natural process (59).

Figure 5. (A) Schematic illustrations of the three types of nanostructures composed of DNA-PAMAM complexes. The “beads-on-string” structure was formed when the dendrimer was in a highly protonated state (a3). (B) The hierarchical self-assembly process of linear DNA with PEG-b-PVP core-shell micelles. Reproduced with permission (55, 58). Copyright 2010, Royal Society of Chemistry. 2012, Wiley-VCH Verlag GmbH & Co. KGaA. 59 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

3.3. DNA-Amphiphile Complexes


One of the problems using nonviral chemical vectors for gene delivery is to facilitate the uptake of nucleic acids through the cellular membrane. Regarding this problem, investigations have been conducted to induce DNA condensation using membrane analogue systems, such as artificially synthesized surfactant molecules or naturally extracted lipids and their derivations. Mixtures of DNA with these amphiphilic molecules provide an important gene transfection strategy and clues for investigating the interactions between DNA and membranes.

3.3.1. DNA-Surfactant Complexes A surfactant or surface-active agent is an amphiphilic molecule that is active at the surface between two phases. It contains both hydrophilic (head) and hydrophobic (tail) parts that can accumulate at the interface between hydrophilic and hydrophobic phases and modify the surface tension. The hydrophobic part is mainly composed of linear or branched alkyl long chains, and the hydrophilic part, also called the polar part, can comprise cationic, anionic, and zwitterionic functional groups. Structures of some typical surfactants are shown in Figure 6.

Figure 6. Chemical formulas of three kinds of surfactants: a cationic surfactant, cetyltrimethylammonium bromide (CTAB); an anionic surfactant, sodium lauryl sulfate (SDS); and a zwitterionic surfactant, dodecyldimethylamine oxide (DDAO). The formation of DNA-surfactant complexes is achieved through attractive Coulomb interactions, and they are stabilized by hydrophobic interactions between the hydrophobic moieties of the surfactant molecules (60). The structures of the DNA-surfactant complexes mainly depends on the surfactant that is used (61). 60 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


The packing parameter (g) of the surfactant; which is the relationship between the head area (a), the extended length (l), and the volume of the hydrophobic part (v), g=v/(lmaxa); determines the physicochemical behavior of the surfactant in water. With the increasing of g value, the surfactants form different assembled structures, from micelles, hexagonal and lamellar to cubic and reversed hexagonal phases to reversed micelles (62). Owing to the negatively charged phosphate DNA backbone, it is common to use cationic surfactants as the complex inducing amphiphiles, and cetyltrimethylammonium bromide (CTAB) is mostly used. The binding between the negatively charged phosphate groups of DNA and the positively charged polar head of a surfactant provides the driving force. Depending upon the preferred shape of the surfactant self-assembly, these complexes can exist in a variety of mesoscopic structures including lamellar (LR) structure, in which the DNA molecules are sandwiched between surfactant bilayers, inverse hexagonal (HII) structure, in which the DNA are confined to the aqueous cores of the micelles, and normal topology hexagonal (HI) structure, in which each DNA is surrounded by cylindrical micelles of DNA (63–66). The schematic models of these structures are show in Figure 7. These complexes show complex phase behavior that depends on multiple factors in addition to the surfactant structure. Additionally, phase transfer can occur within the CTAB-DNA complex by changing the concentration of the cosurfactant or DNA (65, 66).

Figure 7. Schematic representation of (A) the lamellar phase (LR), (B) inverted hexagonal phase (HII) and (C) intercalated hexagonal phase (HI) of a DNA-surfactant complex. Reprinted with permission (65). Copyright 2004 American Physical Society.

It is clear that negatively charged anionic surfactants do not have a significant effect on the conformation behavior of DNA, if the DNA concentration is not sufficiently high. In contrast, zwitterionic surfactants, which exist either in a neutral or cationic protonated form at different pH values, have been proven to have remarkable interactions with DNA. The conformational behavior of linear DNA in the presence of a zwitterionic surfactant, dodecyldimethylamine oxide (DDAO), was examined (67). The positively charged DDAO in the vesicular form behaved as a more efficient DNA-condensation agent than that in the micellar form. 61 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


3.3.2. DNA-Lipid Composition Lipids are one of the most important components in organisms. They are responsible for regulating the passage of biomolecules between cells and within a cell between organelles. Usually, they can be divided into two types: fat-like lipids, which contain ester linkages and long alkyl chains and can be hydrolyzed; and cholesterol- or steroid-like lipids, which do not have ester linkages and cannot be hydrolyzed. The cationic lipids discussed here mainly comprise three basic parts: a charged hydrophilic head group attached to a hydrophobic tail via a linker group, such as an ether, ester, or amide. Their structures are similar to artificially synthesized surfactants but with more complex components as they are often naturally derived. Three kinds of commonly used cationic lipids are listed in Figure 8.

Figure 8. Chemical formulas of three cationic lipids. The co-assembly of DNA and lipids has broadened the investigations on DNA-membrane interactions. Similar to the assembly behavior of surfactants, various structures can be obtained using different lipid structures, including hexagonal (HI), lamellar (LR) and inverse hexagonal (HII) structures. Safinya’s group produced multilamellar-structured CL (cationic liposome)-DNA complexes with alternating lipid bilayers and DNA monolayers by mixing DNA with LCs consisting of DOPC (dioleoyl phosphatidylcholine) and DOTAP (dioleoyl trimethylammonium propane) (68). Then, adding DOPE (dioleoyl phosphatidylethanolamine) lipid or hexanol induced a transition from the lamellar to hexagonal phase owing to the natural curvature (Figure 9a, pathway I) or 62 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


by reducing the membrane bending rigidity (Figure 9a, pathway II) (69). In this phase, the DNA coated with cationic lipid monolayers was arranged on an inverted 2D hexagonal lattice, which is more efficient for gene delivery.

Figure 9. (a) Schematic of two distinct pathways for DNA-lipid complex formation from the lamellar phase to the columnar inverted hexagonal phase with the addition of the DOPE lipid (pathway I) or the addition of helper lipids consisting of mixtures of DOPC and a hexanol cosurfactant (pathway II). (b) Model of the coexistence of two packing modes in the DNA-DOTAP-DOPE system. Most of the DNA is embedded within the lipid columnar inverted-hexagonal assembly, and short, unbound segments of the DNA converge into a condensed toroidal Ψ–structure with a left-handed orientation. Reprinted with permission (69, 70). Copyright 1998, Science. 1999, Federation of European Biochemical Societies.

Chiral DNA packaging was also achieved through the interactions between DNA and cationic liposomes. Zuidam (70) found the B-to-C secondary conformational transition of DNA molecules upon binding to DOTAP, as analyzed using CD spectra. DOTAP-DOPE liposomes affected the collapse of DNA into a tightly packed cholesteric-like phase with long-range chiral order, which coexisted with the inverted hexagonal phase in the DNA-liposome complex; the model is represented as a schematic in Figure 8 b. Electronic interactions were not essential for the formation of the DNA-CL assemblies; the nonionic lipids could also have confined the DNA within the 63 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


reverse hexagonal columnar phases through hydrogen bonds between the polar heads of the lipids and DNA (71). These conditions easily release DNA into excess water. These complexes were able to mimic the gene delivery ability of natural viruses by carrying extracellular DNA across outer cell membranes and nuclear membranes as a nonviral method. The DNA associated within the aqueous channels of the inverse hexagonal (HII) lipids can be actively transcribed by the RNA polymerase (72, 73), and the liquid crystal structure remains during transcription, which demonstrates the potential of using these complexes for transporting genome information. In addition, the DNA-lipid complexes can be prepared as organic-solvent soluble solid films using either cast-stretching methods or the Langmuir-Blodgett (LB) method (74). In the casting method, DNA strands are easily aligned along the stretching direction by casting an organic solution of the DNA-lipid complex onto a substrate or using the hot-press process. In the LB method, the DNA strands are transferred with lipid monolayers at the air-water interface and aligned along the vertical dipping direction. These simple DNA-lipid film preparation methods, which were initially developed by Okahata et al. (75), have promoted the development of DNA-derived functional materials, such as photonic and electronic nanomaterials. 3.4. Dehydrating Agents for Inducing DNA Compaction Aside from the ability of multivalent cations to undergo electrostatic interactions that induce DNA condensation, dehydrating agents that expel DNA single molecules from the water phase have also been proven to efficiently induce the transition of DNA from random coil to compact globule states. Both neutral polymers, such as polyethylene glycol (PEG), poly(2-vinylpyrrolidone) (PVP) and polyacrylamide (PAAm), and poor solvents for DNA, such as ethanol, can be regarded as dehydrating agents.

3.4.1. Neutral-Polymer Induced DNA Compaction In 1971, Lerman (76) discovered that in the presence of over-threshold concentrations of simple neutral polymers (polyethylene glycol (PEG)) and salts, DNA molecules collapse into particles, approaching a compactness similar to that of phage heads. Since then, this strategy, also called crowding-induced DNA condensation, has been studied as a model of DNA condensation in vitro (77–82). The physical mechanism of this phenomenon is caused by depletion interactions between the solution components, usually between different polymers that lack net attractive interactions. Their competition for the solvent space results in phase separation in solution (83). Specific to DNA and PEG, the contacts between these two molecules are considered to be thermodynamically unfavorable. Upon reaching critical concentrations of PEG, the solvent quality for DNA becomes poorer. Therefore, the available free space for the unfolded DNA in solution decreases; thus, DNA undergoes a collapse transition (78). However, while the concentration of PEG is critical for determining the condensation, the degree of 64 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


polymerization and the salt concentration also have a great influence. In addition, analogous to the behavior of polyamines, the condensed DNA can unfold using higher concentrations of PEG (84). These packing/unpacking transitions can be used as a general method for studying the optical properties of the condensed phase of DNA. Jordan et al. (85) developed a volume-exclusion method by adding PEG dropwise into a dilute solution of DNA. The phase segregation was characterized by the appearance of psi-type circular dichroism, which indicated a tertiary structure transition. Similar to using the PEG neutral polymer, a nonionic surfactant solution of polyoxyethylene octylphenyl ether (Triton X-100) with a 50%-90% concentration could also induce the collapse of DNA, which exhibited a discrete coil-globule transition with the increasing concentration (77). The increase in the osmotic pressure of the Triton X-100 solution was attributed to inducing the compaction of the single DNA molecules. In these model systems, the neutral polymers mimic the intracellular globular proteins that do not directly bind to DNA (86). In a crowded medium, the chain molecule can be compcted in a crowded medium, as the depletion forces between monomers would compete with their excluded-volume interaction. This phenomenon is analogous to the chromosome organization in bacterial cells (87). Recently, a polymeric crowder dextran was induced the continuous compaction of DNA in a confined space and a abrupt tranition in a tube-like space (88, 89).

3.4.2. Poor-Solvent-Induced DNA Compaction DNA condensation using a variety of poor solvent conditions is another way to introduce dehydrating agents to induce DNA compaction. The intramolecular association between DNA segments is greater in a poor solvent than in a good solvent. When the density of DNA is high and the frequency of biomolecular encounters is substantial, DNA tends to associate together to form a more concentrated phase. Ethanol is the most commonly used poor solvent to induced phase transitions in DNA. In 1976, Lang et. al (90) directly observed concentrated particles of DNA after using an ethanol treatment through electron microscopy. This method can produce interesting condensed phases of DNA without requiring the presence of other artificial influences, such as proteins and cationic ions. Therefore, this system provides an idea model for analyzing the optical properties of condensed DNA (79, 91, 92). Minsky (93) analyzed the chiral compaction of long linear DNA after the DNA was exposed to a dehydrating EtOH/water mixture under relatively high ionic strength conditions. In this situation, the DNA molecules collapsed into cholesteric-like rod-shaped aggregates in which the DNA folded into parallel arrays. The formation of ordered tertiary DNA enabled efficient longrange interhelical coupling between the nucleotide chromophores, which exhibited nonconservative CD (Figure 10A). Increasing the ionic strength by modulating the salt concentration resulted in a conformation change in the condensed phase from a right-handed handedness to a long-range left-handed handedness through a nonchiral “nematic-like” mesophase, as shown in Figure 10. 65 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 10. (A) CD spectra exhibited by DNA molecules treated with a dehydrating agent (EtOH, 35% v/v) in increasing NaCl concentrations of (1) 0 M; (2) 0.4 M; (3) 0.8 M; (4) 1.2 M; (5) 1.6 M; (6) 2.0 M; and (7) 2.4 M. (B) Schematic representation of chiral rod-like packed DNA molecules and the conformation transition from a right-handed to a left-handed superhelix. Reproduced with persmission (93). Copyright 1998, Wiley-VCH Verlag GmbH & Co. KGaA.

4. Inorganic Mesostructured DNA Assemblies The successful production of mesoporous MCM-41 by Mobil company in Japan in 1992 created a new field for constructing highly ordered mesostructured materials (94, 95). Ordered pore arrangements of mesoporous materials can be achieved using the cooperative assembly of organic template molecules and inorganic sources based on soft-templating synthesis concepts. Although this field started by using artificial soft-templates, such as synthesized surfactants, various kinds of natural biomolecules, such as peptides (96), proteins (97), polysaccharides (98) and even viruses (99, 100), have recently been utilized as templates. Among them, DNA has long been viewed as a soft-template candidate because of its interesting and diverse self-assembly behavior. The fabrication of DNA-templated inorganic materials produces different kinds of mesostructures with various morphologies and structures and provides a better understanding of evolutionary processes, which are difficult to observe directly using organic materials. Although many metal or metal-compound nanomaterials, such as quantum dots, CdS (101) and magnetic Fe3O4 (102), have been constructed using DNA molecules as templates through a biomineralization-like process (103), here, we are mainly concerned with silica inorganic materials with highly ordered mesostructures, in which the production procedure involves both self-assembled condensation and biomineralization processes. 66 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


4.1. DNA-Silica Nanofibers The silica biomineralization of DNA is achieved through the efficient interactions between DNA molecules and the silica source, followed by the hydrolyzation and condensation of the silica species. However, biomimetic silica replications templated by DNA molecules were largely unsuccessful before 2004. In the pH value range that allowed the DNA to maintain its original secondary conformation, the silicate species maintain negative charge, producing electrostatic repulsion with the negatively charged DNA molecules. To conquer the problem, an ingenious strategy was applied by Shinkais et. Al (104), which induced the biomineralization process of DNA by transforming DNA from an anionic into a cationic species in the presence of a two-headed bridge molecule. Rod-like and circular-like silica nanomaterials were obtained using plasmid DNA as a template during a sol-gel polycondensation, as shown in Figure 11.

Figure 11. A) Schematic representation of the transformation of the DNA surface. B) TEM pictures of the obtained Rod-like (b1-b6) and circular-like silica nanomaterials (b7, b8). Reproduced from persmission (104). Copyright 2004, Wiley-VCH Verlag GmbH & Co. KGaA. Che’s group initiated a co-structure directing route to efficiently achieve the biomineralization of DNA molecules as well as their assemblies (105). Typically, functionalized positively charged organic silicane is applied as the CSDA (co-structure directing agent) to electrostatically interact with the negatively charged phosphate groups of the DNA backbones and to co-condensed with the silica source to form the silica framework (Figure 12A). When using N-trimethoxyl-silylpropyl-N,N,N-trimethylammonium chloride (TMAPS) as the CSDA, pore-structure-tunable mesoporous fibers with chiral, ring and ordered nanochannel arrays were transcribed from flexible long DNA molecules and (Figure 12B). The choices on CSDA had a great influence on the assembly mode of the biomolecule; changing TMAPS into 3-aminopropyltrimethoxysilane (APS) would lead to a highly twisted arrangement of DNA molecules because of the inherent chiral properties of DNA (106). The resultant multi-helical mesoporous fibers exhibited three levels of chirality: a primary DNA double 67 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


helix, a mesostructured secondary DNA left-handed orientation and a tertiary microscopic right-handed helical orientation with a twisting-thread morphology (Figure 12C).

Figure 12. (A) Schematic representation of the CSDA route for inducing DNA mineralization. The negatively charged DNA molecules electrostatically interact with the positively charged TMAPS. Then, the co-condensation between TMAPS and the silica source TEOS forms the silica wall that wrapping around the DNA molecules. (B) TEM images of the DNA-silica fibers synthesized using TMAPS as the CSDA. The image contrast shows the inner channels casted from parallel (b1) or twisted (b2) long DNA molecules. (C) SEM (c1 and c2) and TEM (c3) images and the model (c4) of the chiral DNA-silica fibers with hierarchical chirality using APS as the CSDA. Reproduced with permission (105, 106). Copyright 2009, 2013, Royal Society of Chemistry. 68 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.

4.2. DNA-Silica Nanoparticles


As mentioned above, as a semi-rigid polymer, the stiffness of DNA is quantified by its persistence length (usually 50 nm), which greatly influences the assembly behavior of the molecules. These DNA fragments approach or are shorter than the persistence length, which can be viewed as rigid rods, and will more likely form liquid-crystal phases, which agrees with Onsager’s theory on rigid rod-like polymer assembly (107). The biomineralization of multiple liquid-crystals will highly expand the types of high-ordered structures of inorganic mineralization materials.

4.2.1. DNA-Silica Plates with p4mm Structure Lattices The silica biomineralization of the mesophase of short rigid DNA was first achieved by Che et al. (23) Similar to the strategy used during the formation of DNA-silica fibers, TMAPS was applied as the CSDA to bridge the biomolecular templates and the silica source. The other critical role of TMAPS was to act as a condensation agent to screen the electrostatic repulsions between the negatively charged DNA and to induce the highly ordered packing. The resulting DNA-silica composites exhibited a hexagonal platelet morphology with a thickness corresponding to the length of the template DNA molecules (Figure 13a1 and a3). The silicification of the DNA packing structure produced a mesoporous structure with a rare p4mm supra lattice. The fourfold symmetrical mesochannels with a long axis vertical to the platelets are rarely seen in naturally occurring DNA mesophases (Figure 13a2 and a4). Surprisingly, the morphology of the platelet was not square, which was inconsistent with its crystalline structure. Subsequent precise observations and analyses on the growth process have resulted in the following explanations (108). The formed hexagonal platelet morphologies coincided with the silicatropic DNA liquid crystal 2D hexagonal p6mm mesophase during the initial stage of the reaction. Then, a transition from the p6mm to p4mm structure inside the platelet occurred during the silica condensation, along with a decrease in the distances between the DNA molecules because of the changing charge densities of the reactants. These phenomena caused the DNA molecules to pack densely, which was attributed to the electrostatic interactions or “zipper” that pulled the molecules together (Figure 13b). The p4mm domains, which prefer a specific, smaller interaxial separation, were energetically favored. The flexible properties of the silica framework before the complete copolymerization enabled the transitions while maintaining the hexagonal morphology. This investigation regarding the phase transitions that occur during the solidification of the DNA mesophase provides a feasible observation model for studying the condensed phases of DNA and provides a new general method for the formation of more materials with exceptional structures and morphologies. 69 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Figure 13. Morphologies and structures of the DNA-silica platelets. (a1) SEM images showing the hexagonal morphology of the platelets. (a2) and (a3) HRTEM images taken from the top and side of one typical platelet and the corresponding Fourier diffractograms showing the p4mm structure. (a4) Electrostatic-potential maps of the p4mm structure (23). (b) An illustration of the 2D-hexagonal to 2D-square transformation (108). Reproduced with permission (23, 108). Copyright 2009, Wiley-VCH Verlag GmbH & Co. KGaA. 2013, American Chemical Society.

4.2.2. Chiral DNA-Silica Impellers The chiral self-assembly of DNA into mesophases is an important feature of DNA molecules owing to their inherent chiral properties. Several types of interwound chiral conformations during DNA compaction have been found in organisms, such as bacterial plasmids and sperm heads, which are also intriguing for artificial systems in vitro. During the formation of achiral DNA-silica plates, the “zipper” lattice happens under a subtle electrostatic interaction balance. As mentioned above, competition exists between the densely packed constraints and the ability to twist along the chiral order, which determines the properties of the final assembled structure of the DNA. Therefore, a small disturbance in the synthesis system can break the balance and induce structural fluctuations. Chiral DNA-silica assemblies (CDSA) were obtained by introducing divalent alkaline earth ions (Mg2+) into a DNA-silica synthesis system, which produced 4 μm diametrical impeller-like particles with 100-nm thick blades (Figure 14A) (109). 70 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


Clockwise (marked as R-CDSA) or anticlockwise (marked as L-CDSA) blade stacking in a circle corresponded to the left-handed and right-handed handedness, respectively. Structural analyses revealed that the distorted 2D-square p4mm mesostructure of a typical blade with right-handed CDSAs twisted along the (01) lattice in a left-handed manner, as illustrated in the model in Figure 14B. From the model, one can clearly distinguish the coexistence of hierarchical chirality with opposite handedness. For instance, the R-CDSA with clockwise rotated blades is composed of left-handed chiral distortion p4mm layers and right handed helical array viewed along longitude axis of DNA molecules. Strong CD signal peaks at approximately 230 and 295 nm were attributed to the existence of DNA long-range chiral packing, similar to the nonconservative ellipticities exhibited during chiral cholesteric organization. The final CD signals of the material exhibited overlapping results owing to different responses of circular polarized light from the two opposite chiral structures. Since the presence of water greatly determined the secondary conformations of the DNA, which determined the chromophore coupling in the right-handed helical array, the materials exhibited water-dependent CD signal reversion (Figure 14C), implying their potential to be applied as humidity sensors (110). Interestingly, the synthesized system of CDSAs had a certain flexibility in that the molar ratio of the cationic silanes, temperature and pH values could influence the resulting handedness, which was also reflected in the DRCD spectra (Figure 14B). This flexibility was because that the origin of chirality in the dislocation arrays of the DNA is due to the charge mismatched “ion-bridging” between the DNA molecules and polyamine in the presence of divalent alkaline earth metal ions. Hence, another kind of competition existed during the formation of the CDSAs (111). This competition occurred between two interactions, the electrostatic interactions of the DNA-divalent metal ions and the electrostatic interactions of the DNA-polyamine complexes. Both the Mg2+ and amino species induced chirality but had opposite effects; right-handed handedness was favored by Mg2+, while left-handed chiral phases were favored by the latter (112). Thus, the handedness inversion occurred under proper conditions. 4.3. DNA-Silica Films 4.3.1. Patterned Achiral DNA-Silica Films Patterned DNA-silica films were obtained after the anchoring growth of DNA-silica plates on positively charged silicon substrates (113). This process exhibited interested surface behavior when the DNA-silica complexes were epitaxially grown on a substrate full of electronic charges. During the formation of the DNA-silica film, a strategy was used to align, place and arrange the DNA-silica plates on the patterned silicon substrate. The main method in this strategy was to thermodynamically and kinetically control the ionization degree of the DNA, TMAPS and quaternary ammonium groups at different locations of the lithographically patterned silicon surface, which was influenced by geometry effects (substrate grooves, protuberances and edge areas). As seen in Figure 15, by controlling the pH, TMAPS concentration and the lithographic patterning of 71 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


the silicon substrate, the alignment (Figure 15a), placement (Figure 15b and c) and arrangement (Figure 15d) of the epitaxially grown DNA-silica plates could be selectively controlled to form different types of patterned films.

Figure 14. Morphology and optical activity of the impeller-like HDSAs. (A) SEM images of R-CDSAs and L-CDSAs synthesized at 0 °C and 25 °C, respectively. (B) Schematic model showing the hierarchical chirality of the opposite handedness orientations from different viewpoints. (C) DRCD spectra of the HDSAs synthesized under different temperatures of (a) 25 °C, (b) 15 °C, (c) 8 °C, (d) 4 °C and (e) 0 °C measured in dry (dotted line) and wet states (solid line). Reproduced with permission (109, 110). Copyright 2011, 2013. Wiley-VCH Verlag GmbH & Co. KGaA.



Figure 15. Alignment, placement and arrangement of DNA-silica platelets on a lithographically patterned silicon surface with horizontal (a) or vertical epitaxial growth (b-d). (a) Alignment of DNA-silica plateltes on a silicon surface with horizontal epitaxial growth. (b-d) Positions of the selectively grown platelets influenced by the geometry of the silicon surface, in which the placement was influenced by the grooves (b), protuberances (c) and edges (d), respectively. Reproduced with permission (113). Copyright 2013. Wiley-VCH Verlag GmbH & Co. KGaA.

4.3.2. Chiral DNA-Silica Films The epitaxial growth of impeller-like chiral DNA-silica assemblies on silicon substrates resulted in chiral DNA-silica films that were composed of right-handed, vertically aligned semi-CDSAs (Figure 16a1) (114). The absorption effect of chromophore coupling within the DNA chiral packing and the circular Bragg resonance of the macroscopic impeller architecture induced absorption-based optical activity in the UV wavelength range and scattering-based optical activity that extended to the visible wavelength range, respectively. The CD signals in the scattering wavelength range were tuned by varying the average refractive index and helical pitch, according to the circular Bragg reflection equation (Figure 16a2). Furthermore, in order to meet the requirement of building highly ordered chiral films, a “quartet templating” method was constructed to guide chiral silica nanostructures arranged on crystalline mica surfaces (Figure 16B) (115). Owing to the bridging role of Mg2+, which could anchor to the (100) hexagonal symmetrical crystal surface of mica, an ordering transfer occurred from the “mica-Mg2+-DNA-silica” pathway, which produced densely grown chiral blades with a uniform orientation. This approach may provide a facile strategy for fabricating large-scale functional devices.



Figure 16. Morphologies and optical activity of the chiral DNA-silica films. (A1-2) SEM (A1) and DRCD/UV-Vis spectra (A2) of the randomly distributed chiral DNA-silica film that was grown on a silicon substrate. The DRCD spectra present the signals from the as-made film (red line), the calcined film (blue line) and the film after immersion in water (dotted line). B1-2) SEM (B1) and DRCD/UV-Vis spectra (B2) of the uniformly distributed chiral DNA-silica film that was grown on a mica substrate. The DRCD spectra presents the signals from the densely distributed film (black line), sparsely distributed film (red line) and random achiral film (blue line). (C) Photography (C1) and DRCD/UV-Vis spectra (C2) of the freestanding chiral DNA-silica film. The colored lines in the DRCD spectra correspond to the colored backgrounds. Reproduced with permission (114–116). Copyright 2014, Nature Publishing Group. 2016, Wiley-VCH Verlag GmbH & Co. KGaA. 2015, American Chemical Society.

In the absence of substrates, because of the film-forming ability of DNA and the high flexibility of organic silanes with long alkyl chains, pliable free-standing DNA-silica films were obtained by the silicification of the DNA condensed phase in the presence of a packing agent and CSDA, APS, using the evaporation-induced self-assembly process (116). The obtained antipodal films had a semitransparent appearance and exhibited broadband DRCD spectra when measured with a black background because of the long-range coupling and strong scattering effect of the domains of the semi-cholesteric DNA liquid crystals (Figure 16C, black line). The signals that originated from the scattering effect could be easily tuned to various narrow-band signals by changing the absorption bands of the backgrounds or by introducing colorful chromophore dye molecules into the film (Figure 16C, colored line). 74 Ito et al.; Advances in Bioinspired and Biomedical Materials Volume 1 ACS Symposium Series; American Chemical Society: Washington, DC, 2017.


5. Conclusion Inspired by nature, various kinds of methods for inducing ordered and highly compact phases of DNA have been developed through the use of naturally extracted or artificially synthesized DNA condensation agents. The studies of DNA condensation in vitro have provided simplified models for investigating the complex DNA condensation mechanisms in vivo and have further triggered the formation of various kinds of novel organic and inorganic mesostructured materials. The formation of these materials has enabled great progress in both biology and materials fields. The biggest achievements have been made for improving gene delivery technology, resulting in higher delivery efficiencies, facilitated gene uptake, and the timely release of the genes within targets. In addition, in the materials field, the ordered phases of DNA-related materials have shown many potential applications in electronics and optical fields (117–119). DNA-related optical materials possess better stability, higher optical-damage thresholds and low optical propagation losses, and can be considered as a new generation of photonic materials (120, 121). In the electronics field, DNA molecules can also act as semiconductors with a wide energy gap (122); in addition, the electrical conductivity of doped DNA-based systems exhibits typical ionic characteristics. The combination of these attraction properties of DNA and the ordered arrangements of mesostructured materials could give rise to fascinating high-tech applications, such as electronic chips, biosensors, electron guides and optical polarizers.

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