Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single

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Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single-Walled Carbon Nanotube: a Computational Study Soumadwip Ghosh, and Rajarshi Chakrabarti J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.6b02035 • Publication Date (Web): 05 Apr 2016 Downloaded from http://pubs.acs.org on April 12, 2016

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The Journal of Physical Chemistry

Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single-Walled Carbon Nanotube: a Computational Study Soumadwip Ghosh, Rajarshi Chakrabarti* *

Email: [email protected]

Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai – 40076, India.

ABSTRACT: Xeno-nucleic acids are synthetic nucleic acid analogues which are potential candidates for antisense or antigene therapy owing to their higher thermal and enzymatic stability compared to that of naturally occurring ones at physiological conditions. We investigate the binding and unzipping of Xylonucleic acid (XNA) containing xylose (a stereoisomer of ribose) sugar in its backbone assisted by a single walled carbon nanotube (SWCNT) using extensive atomistic molecular dynamics simulations. Our simulations confirm XNA to undergo faster unzipping compared to a double stranded RNA with the same nucleobase sequence which is presumably due to the near orthogonal base pairing arrangement of the constituent nucleobases of XNA at physiologically relevant conditions (in terms of temperature and salt concentration). The interaction between XNA and SWCNT mimics that of a small interfering RNA (siRNA) and RNA – induced silencing complex (RISC) during a typical RNA induced gene silencing process where the duplex chain unwinding of the siRNA is of primordial importance. Our study may find relevance in designing a more efficient and safer delivery platform for xeno-nucleic acids by grafting these RNA analogues to SWCNT into an infected target cell. This unveils promising applications of XNA in the field of gene delivery for antisense therapies.

I. INTRODUCTION: Xeno-nucleic acids1 are artificial nucleic acids differing in the compositions of aromatic bases, phosphate backbones or the sugar linkages from the naturally occurring ones. Synthetic modification of any of the above nucleic acid components can drastically influence the base stacking and the stability of the Watson-Crick hydrogen bonds existing between the two parallel chains of a nucleic acid duplex enabling them to store genetic information. Along this line, recent developments in the field of xenobiology include the synthesis of peptide nucleic acids (PNA), (LNA),

3

Phosphorothiolates,

4

hexitol nucleic acids (HNA),

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2

locked nucleic acids

glycol nucleic acids (GNA) 6,

cyclohexenyl nucleic acids (CeNA), 7 arabino nucleic acids (ANA) 8 and threose nucleic acids (TNA). 1 ACS Paragon Plus Environment


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In particular, there has always been a search for artificial nucleic acids having engineered backbones

and naturally occurring nucleobases with novel functionalities. These have mainly been studied in the context of the origin of life. 10, 11 Among other works, xeno-nucleic acids have been used as molecular beacons for the sensitive detection of nucleic acids.

12

Holliger and co-workers have made HNA

based enzymes capable of binding and destroying RNA at specific sites.

13

Recently, Maiti and co-

workers have synthesized a xylonucleic acid containing a potentially prebiotic xylose (wood) sugar in its backbone and they have demonstrated the structural uniqueness of the molecule mentioning that it adopts an extended helical geometry and the orthogonal arrangements of complementary base pairs on opposite strands restrict its ability to interact with an unbiased sequence of a DNA/RNA.

14

These

authors have acknowledged its potential merit of being useful as an orthogonal genetic system in synthetic biology. Motivated by the above work, we attempt to study the interaction between xylonucleic acid (XNA) and a single-walled carbon nanotube (SWCNT) which is an efficient transporter for nucleic acids and drug molecules into human cells. 15, 16 Numerous experimental 17-19 as well as computational

20-24

studies have established the fact that SWCNTs and nucleic acids make

stable hybrids by means of dispersive π – π stacking and hydrophobic interactions. However, to the best of our knowledge the interaction between carbon nanotube and a novel nucleic acid analogue has not been investigated at the atomistic level. In this paper, we address two important aspects. First, using atomistic molecular dynamics we show that the unzipping kinetics of XNA is faster than that of RNA having identical nucleobase sequence at 300K temperature and a low concentration of salt (35 mM NaCl). This seems to be a consequence of the significant weakening of the Watson – Crick pairing between complementary base pairs residing in the parallel chains of the XNA duplex. The weakness of the XNA hydrogen bonds compared to that of the RNA can be attributed to (i) the orthogonal base paring arrangements in XNA that affects the optimal helical geometry adopted by the duplex and (ii) the conformationally strained phosphate backbone composed of a C3’ epimer of ribose in its sugar units.

14

On the other hand, the RNA molecule possesses coplanar base pairs and a more

flexible phosphate backbone which ensure its optimal helical stability which, in turn, is responsible for its structural superiority over XNA. Second, we perform additional simulations at 310K temperature and 150 mM concentration of NaCl separately in an attempt to extrapolate physiological relevance by closely mimicking the conditions existing inside a human cell.

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These additional

simulations demonstrate the same trend of more rapid unzipping of XNA compared to that of RNA induced by a SWCNT at physiologically ambient temperature and salt concentration. Our study finds relevance in a typical RNA induced gene silencing technique, popularly known as RNA interference (RNAi)

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where the duplex chain unwinding of a chemically modified small interfering RNA

(siRNA) induced by RNA – induced silencing complex (RISC) feasibility of the overall process.

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is critical in determining the

The RISC is comprised of ribonuclease protein Dicer which

triggers the production of siRNA species from relatively longer double stranded RNAs (dsRNA) while other components like Argonauate2 and siRNA binding protein facilitate the siRNA duplex 2 ACS Paragon Plus Environment

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unwinding.

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After integration into the RISC, the single stranded siRNA bases anchor on to the

messenger RNA (mRNA) of the fatal gene, cleave it and thereby preventing it from being used as a translational template.

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In spite of the inherent merits of RNAi for controlling the expression of

potentially fatal genes, there are several limitations. One of the major limitations is the degradation of chemically unmodified nucleic acid substrates in human serum.

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Our study is capable of providing

comprehensive evidence for the chain unzipping of a thermally and enzymatically more sustainable RNA analogue on the surface of a transfecting carrier

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such as carbon nanotube at physiological

conditions and thus assuring a long-term and more efficient protection against gene expression without chemical degradation of the substrate. Along this line, Kalota et al. has shown that 2-deoxy-2fluoro-Darabinonucleic acid (2F-ANA) sugar modifications of the oligonucleotide help maintain high intracellular concentrations for prolonged periods of time leading to long-term gene silencing due to its higher binding affinity with the target mRNA.

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Similarly, Elmén et al. has shown that the

incorporation of LNA enhances the serum half-life of siRNA in the context of developing a bio-stable therapeutic platform.

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However, only a handful of nucleic acid mimics has been found to be

tolerated in gene replication and transcription in bacteria for synthetic biology.33 We speculate that an artificially synthesized XNA can be useful in silencing genes responsible for diseases such as Cancer and HIV 34, 35 and help resolving the challenges encountered in gene delivery processes.

II. Computational Details

All the molecular dynamics (MD) simulations are performed using GROMACS 4.5.6 combination with the all atom CHARMM 36

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36

in

force field with CMAP corrections for improved

dihedrals for proteins. The PDB file for the xylonucleic acid (PDB ID 2N4J) deposited by Maiti and co-workers

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was directly obtained from the Brookhaven protein data bank

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and was used without

any further modification. The sequence for the XNA used is 5’-xGUGUACAC-3’ sequence 5’-rGUGUACAC-3’ is generated using the make-NA server

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and the RNA

from James Stroud’s group.

Explicit TIP3P (transferable intramolecular potential three point) water model

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is used for solvating

the nucleic acids. The topology for each nucleic acid is made using the pdb2gmx utility of GROMACS.

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We build the initial periodic structure of a (15 x 15) armchair single-walled carbon

nanotube (diameter = 2.15 nm, length = 7 nm) using the nanotube builder utility of VMD 1.9.2.

41

We

choose the CNT large enough to ensure sufficient sliding length for the nucleic acids before attaining a stable bound state. The carbon atoms of the nanotube are modelled as uncharged Lennard-Jones particles using sp2 parameters of graphitic carbon atoms according to literature.

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The initial

configuration of each of the simulation systems is prepared by keeping the XNA / RNA very close to the SWCNT surface with the carbon nanotube and the nucleic acid helix axes being almost parallel to each other inside a cubic box of dimension 8.70 x 8.70 x 8.70 nm3. Subsequently, the entire

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simulation box is filled with 19432 TIP3P water molecules and a total 14 Na+ ions are added for the charge neutralization of both XNA and RNA phosphate backbones in two separate MD simulations. This corresponds to the salt concentration of the system to be 35 mM roughly. We carry out additional MD simulations for both XNA and RNA in the presence of 150 mM NaCl, i.e. the physiologically realistic concentration of NaCl inside a human cell. For this purpose, we introduce a total number of 56 Na+ and 42 Cl- randomly into the system containing XNA and 19334 water molecules (similarly, 53 Na+ and 39 Cl- for the system containing RNA and 18498 water molecules). In order to study the unzipping kinetics at a physiologically more relevant temperature (310K) we also run two separate simulations for both XNA and RNA. The logic behind carrying out simulations at a low (35 mM) and a high (150 mM) concentration of NaCl is to determine the difference in the unzipping patterns of XNA and RNA (if any) assisted by SWCNT in two different environments across an ideal cell membrane represented by a pre–existing salt concentration gradient which might affect the binding affinity of the two types of nucleic acids under study for the rigid SWCNT. 43

First we employ 1000 steepest descent

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energy minimization steps. Next a position-restrained

dynamics is carried out on the system at constant volume and temperature (NVT) for 500 ps where the temperature of the system is slowly raised to 300 / 310K using weak 20 Kcal/mol Å2 harmonic constraints on the solutes in the initial structure. The system is then equilibrated at constant pressure (1 bar) and temperature (NPT) performed at a temperature of 300 / 310K for 5 ns (0.5 ps time constant for heat bath coupling and 0.5 ps pressure relaxation time). Properties such as pressure, cell volume and density converge well to their desired values within this period of equilibration. The NPT step is carried out using Parrinello-Rahman barostat

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and the V-rescale thermostat

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is used to keep

the temperature of the system constant at 300 / 310 K and the system configuration is updated using the leap frog integrator for integrating the Newton’s motion of equation.

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After that, the production

MD run is started for 100 ns. The entire production MD is carried out with a time step of 2 fs and the information regarding trajectory, velocity and energy is recorded after each 5 ps for trajectory analysis. The minimum image convention

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is used to calculate the short ranged Lennard–Jones

interactions. The spherical cut-off distance for both electrostatic as well as van der Waals forces is kept at 1 nm. We have used periodic boundary conditions in all three directions and the SHAKE

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algorithm is used to constrain the bonds to the hydrogen atoms of the water molecules. The long range electrostatic interactions are calculated using the particle mesh Ewald (PME) method

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using a cubic

B–spline interpolation of order 4 and a 10-5 tolerance is set for the direct space sum cut-off. The specific base pairs of interest are tagged as energy groups before starting each MD run. Snapshots for visualizing the trajectories are rendered using VMD. 41 We generate six independent trajectories (each simulation repeated twice for error estimation and reproducibility) representing various simulation conditions in this study. Each of the repeat simulations was performed with the identical initial


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simulation set up without moving any of its components. A brief overview of each one of the simulated systems is given in TABLE T1 in the supporting information.

(a)

(b)

FIG.1. Chemical representation of the sugar – phosphate backbones of (a) XNA and (b) RNA respectively

The above chemical representation displays the stereo chemical inversion in the C3’ carbon atom of the sugar ring in XNA (Figure 1a) with respect to RNA (Figure 1b). Apart from this, the rest of the structural constituents such as the nucleobase arrangements are identical for both of the above two species.

III. Simulation Results and Discussions 5 ACS Paragon Plus Environment


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(c)

(d)

(f)

(e)

(g)


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(h)

(i)

(j)

(k)

FIG.2. VMD 41 Screenshots of (a) the Xylonucleic acid structural framework as obtained from the PDB 2N4J, 14 Initial simulation systems containing (15 x 15) SWCNT and (b) XNA, (c) RNA. Horizontal view of (d)-(g) the XNA-SWCNT and (h)-(k) RNA-SWCNT hybrids at different intervals of the simulation at 300K temperature and 35 mM NaCl concentration. The RNA / XNA are represented by Licorice models while VDW representation has been chosen for the CNT. The nucleic acid counterions and water molecules are ignored for clarity.

From Figure 2a and b one can easily point out the highly inclined nature of the nucleobases in the initial structure of the XNA molecule with respect to its backbone whereas the complementary base pairs on the opposite strands of the RNA duplex seem to be almost coplanar (Figure 2c). Figures 2d-g show the extent of breaking of the native Watson – Crick hydrogen bonds in XNA to be higher than that of the RNA (Figures 2h-k) as the simulation time progresses at a much less stringent physiological condition. The relative extent of binding and chain unzipping in the XNA and RNA assisted by the SWCNT (at 300K temperature and 35 mM salt concentration) is illustrated in the next sections.

A. Formation of Stable Hybrids between XNA and SWCNT

The above snapshots (Figure 2) provide primary evidence of the XNA molecule getting adsorbed on the surface of the rigid SWCNT and then undergoing unzipping at different instants of simulation. In



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order to understand the broad microscopic picture of such binding we calculate the numbers of XNA atoms that come close the SWCNT as a function of simulation time within a specified distance cutoff. The number of contacts formed between the XNA and the SWCNT (Nc) has been computed by imposing a cut-off of 5 Å according to the following expression.

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Similarly, we calculate Nc for

RNA with identical nucleobase sequence at the same simulation condition and plot them together for comparison. 𝑁𝑆𝑊𝐶𝑁𝑇 𝑁𝑁𝐴 𝑟 𝑖 +5Å

𝑁𝑐 𝑡 =

𝛿 𝑟 𝑡 − 𝑟𝑗 𝑡 𝑖=1

𝑑𝑟

(1)

𝑗 =1 𝑟 𝑖

Where 𝑁𝑆𝑊𝐶𝑁𝑇 and 𝑁𝑁𝐴 are the total number of atoms in CNT and the nucleic acid (XNA / RNA) respectively, and, 𝑟𝑗 is the distance of the 𝑗 𝑡ℎ atom of the corresponding nucleic acid from the 𝑖 𝑡ℎ atom of the CNT. It can easily be observed from Figure 3a that the number of close contacts between the two species keeps on increasing almost throughout the entire simulation for both XNA and RNA and then show some signature of saturations. However, at any given point the computed Nc is higher for XNA (black line, Figure 3a) as compared to that of RNA (red line, Figure 3b) at identical simulation conditions. The delayed initiation of contact formation in the case of RNA might serve as a preliminary evidence for its poor binding affinity for the carbon nanotube compared to XNA. We also calculate the average root mean square deviation (RMSD) for estimating the conformational deviation of each nucleobases (number 1 – 16) belonging to either XNA or RNA from their respective native structures. The estimated RMSDs cover the whole simulated trajectory excluding the hydrogen atoms. It immediately follows from Figure 3b that majority of the nucleobases constituting XNA (black histograms, Figure 3b) experiences higher conformational fluctuations than RNA (red histograms, Figure 3b) at identical simulation conditions although they have the same sequence of nucleobases. We also calculate radial distribution functions between the centres-of-mass of the nucleic acids and the SWCNT for the sake of better visualization in the differences observed in base proximity to the CNT surface (Figure S1, Supporting information). It seems that the XNA bases prefer the SWCNT sidewall more than that of the RNA at similar simulation conditions which correlates well with Figure 3a.


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(a)

(b)

FIG.3. (a) Number of close contacts (Nc) of nucleic acid (XNA / RNA) atoms within a cut-off of 5 Å from the CNT surface and (b) average RMSD for individual base residues of both XNA and RNA with respect to its native conformation at 300K temperature and 35 mM concentration of NaCl.

B. Comparison of the Binding Energy of XNA and RNA on SWCNT Surface

The extent of a duplex nucleic acid unzipping is a function of its interaction with the carbon nanotube. According to previous studies, the binding of a flexible single stranded DNA on the surface of a more rigid CNT is controlled by factors such as the diameter of the carbon nanotube, nucleic acid

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and the salt concentration of the medium.

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the sequence of the

Things are slightly different for a

structurally more rigid double stranded nucleic acid where the main stabilizing force is attributed to the Watson – Crick hydrogen bonds between complementary base pairs residing in the two opposite strands. Along this line, Alegret and co-workers have shown the complete disruption of a short double stranded DNA (dsDNA) into two separate chains due to its interaction with the sidewall of a SWCNT on a relatively short simulation time scale.

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Lu and co-workers have demonstrated the fitting of

periodic (10, 0) carbon nanotubes in the major groove of a sufficiently long B-DNA which may be applicable as a device for ultrafast DNA sequencing.

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Zhao has shown the importance of dispersive

π – stacking interactions between the hydrophobic DNA bases and the graphitic carbon atoms of both CNT and graphene in determining the stability of the self assembled DNA segments on these nanoscale materials in aqueous environment.

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Illiafar et al. has also shown that the interaction of an

ssDNA with curved carbon nanotube is much stronger than with flat graphite using single molecule force spectroscopy.

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In this study, we calculate the short range average interaction energies (Eint)

between each base residues (of XNA / RNA) and CNT averaged over the entire trajectory (Figure 4a) in order to estimate the overall feasibility of binding between the two species under consideration at a relatively less harsh physiological condition. Eint is determined using the electrostatic and van der Waals cut-offs already mentioned in section II. The van der Waals counterpart of the Eint accounts for the dispersive π-π stacking interactions, at least qualitatively since the actual magnitude of π-π stacking cannot be obtained unambiguously from classical dynamics because the classical force fields are unable to treat the polarizability of the π electrons explicitly.

58, 59

It immediately follows from



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Figure 4a that most of the nucleobases (1 – 16) of XNA exhibit more negative average Eint values (black points) as compared to that of RNA (red points) indicating better non – covalent interactions of the former species with CNT within the given error bars. This is due to closer proximities of XNA bases to the CNT surface than those of the RNA as revealed by Figure 3a. It is worth mentioning here that Xylo – configured oligonucleotides exhibit unusual structural and thermodynamic features which affect their hybridization towards DNA or RNA complements.

61, 62

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Moreover, the cumulative

Eint value for the duplex nucleic acid is in close agreement with a recent experimental work by Shiraki et al. 63 In order to correlate the outcomes of Figure 3a convincingly we also calculate the free energy of nucleic acid – SWCNT binding, F(r) as a function of the intermittent distance between the centres – of – mass (COMs) of two different nucleic acids and the SWCNT throughout the whole simulated trajectory separately (Figure 4b). We employ the following equation to calculate F(r) 𝐹 𝑟 = −𝑘𝐵 𝑇 ln 𝑃(𝑟)

(2)

Where, P(r) is the probability of finding the XNA / RNA at a given position r from the CNT. Here, r is the distance between the COMs of the XNA / RNA and CNT respectively, kB is the Boltzmann constant and T is the temperature of the system. We would like to mention that the above qualitative analysis resembles the work by Mogurampelly et al. where the binding free energy of individual neucleobases adsorbed on a flat graphene sheet has been qualitatively obtained from the histograms of their closest approach

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as techniques such as free energy perturbation

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or umbrella sampling

would be computationally expensive for a system like ours and thus have not been attempted in the present study.

(a)

(b)

FIG.4.(a) Average non-bonded interaction energy of individual bases (along with standard error bars) of both the nucleic acids with SWCNT and (b) the free energy of each nucleic acid - CNT binding as a function of the separation between their COMs respectively at 300K temperature and 35 mM NaCl concentration.


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It is evident from Figure 4b that XNA binds more favourably with CNT surface than RNA. The contact pair minima appear around -9.136±0.091 and -6.382±0.120 kJ/mol for the black and the red curve respectively indicating a much weaker binding of RNA on the surface of the carbon nanotube than XNA. The standard deviations are calculated from two independent simulations at each of the above mentioned conditions. The findings of Figure 3 and 4 are consistent with each other in the sense that both of them illustrate higher propensity of neucleobase stacking to the SWCNT in the case of XNA as compared to RNA. Very high affinity of the nucleic acid bases for the nanotube causes structural deformations in both the duplexes which undergo rapid unwinding of the Watson – Crick hydrogen bonds between the complementary base pairs residing in opposite strands as the simulation time progresses. The higher magnitude of binding interaction between SWCNT and XNA than that of RNA is also reflected in the number and the distribution of hydrogen bonds for the two different types of nucleic acids in this study (section III.C).

C. Unzipping of the Watson – Crick (WC) Hydrogen Bonds The hydrogen bonds between the two strands confer stability to a nucleic acid duplex by providing them a well-defined three dimensional structure and enabling it for gene storage. The unzipping of such RNA hydrogen bonds is of crucial significance in a cellular RNAi technique since one of the unzipped RNA single strands specifically binds with the mRNA and thus reduces the gene expression. 67

In an attempt to study the comparative unzipping kinetics of XNA and RNA we calculate the time

evolution of the number of native inter-strand hydrogen bonds (Figure 5a) using the g_hbond utility of GROMACS 4.5.6.

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A geometric criterion is followed to define a hydrogen bond between a donor

and an acceptor. 68 A hydrogen bond is considered being formed when the distance between the donor and acceptor is ≤ 0.35 nm and the donor-hydrogen-acceptor bond angle is ≤ 300 at a fixed temperature as per as the usual norm found in the literature.

69

Figure 5a suggests that around 20 ns of the

simulation almost 60% of the native hydrogen bonds are broken for RNA (red line) whereas only 10% of the XNA hydrogen bonds survive (black line) in this time window. Figure 5a also indicates a higher number of intact WC hydrogen bonds of RNA as compared to that of XNA at the end of the simulation. This observation is indicative of the inherently weaker nature of the WC hydrogen bonds in XNA compared to that of RNA which can be rationalized by comparing the hydrogen bond length (Figure 5b) and bond angle (Figure 5c) distributions between the two nucleic acids under consideration. We observe that the inter – strand H-bond length distribution is shifted towards smaller H-bond length between the donors and the acceptors indicating the strengthening of H-bonding interactions in case of RNA (dotted red line) duplex as compared to that of XNA (black line, FIG 5b). Similar insights can be drawn from Figure 5c where the donor – hydrogen – acceptor bond angle for RNA is shifted to a slightly smaller value (dotted red line) compared to that of XNA (black line). These observations complement the higher extent of binding interactions of XNA with SWCNT as compared to that of RNA addressed previously (section III.C). 11 ACS Paragon Plus Environment


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(a)

(b)

(c) FIG.5. (a) Time evolution of the number (b) bond length and (c) bond angle distributions of the inter – strand WC hydrogen bonds for two different nucleic acids at 300K temperature and 35 mM concentration of NaCl.

D. Spatial Density Distribution Functions

We calculate the spatial density distribution functions (SDF) of the two nucleic acids around the time –averaged SWCNT using the g_spatial utility of GROMACS 4.6.5

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which computes the three

dimensional density distribution of a certain species in the vicinity of the other by reading the entire trajectory. For the best display, the SDFs are drawn for equal densities (isovalue ~ 150) in each case. The time – averaged distribution of both the nucleic acids (represented as blue isosurfaces) under study around the rigid carbon nanotube (Figure 6a – d) (represented as silver coloured van der Waals spheres) is more helpful in interpreting the broad dynamic picture of interaction between the two species than the corresponding snapshots at a particular instant of the simulation (Figure 2) since the former approach takes into account the entire trajectory. From Figure 6a – d it is quite apparent that the density of XNA around the CNT is relatively higher than RNA which, in turn, correlates well with


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the higher binding affinity of XNA for carbon nanotube, compared to that of RNA (section III.B and C).

(b) XNA

(a) XNA

XNA

(c) RNA

(d) RNA

FIG.6. (a) & (c) The horizontal, (b) & (d) the front views of the SDF of XNA and RNA (blue isosurfaces) respectively around the time-averaged CNT structures (silver coloured van der Waals sphere) at 300K temperature and 35 mM NaCl concentrations. The snapshots are rendered using VMD 1.9.2. 41 The solvent molecules and Na+ ions are not included for clarity.

E. Effect of Increasing Temperature and Salt Concentration It is well known that the flexibility of a single stranded nucleic acid is sensitive towards its ionic environment medium.

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and can adopt different conformations depending on the salt concentration of the

We have recently shown that the binding of a nucleotide containing 12 bases with a

SWCNT gets significantly weakened at a higher ionic strength of the medium owing to the self – stacking of the nucleobases.

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Although primary and secondary hydrogen bond interactions between

complementary base pairs appear to be the main stabilizing factor

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, ionic properties such as ion

concentration, charge and size also play vital roles in determining the helix stability and folding kinetics of duplex nucleic acids. 73, 74 In general, cations stabilize the duplex DNA by neutralizing the 13 ACS Paragon Plus Environment


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negatively charged phosphate backbone and thus help it to adopt a more compact native structure.

75

On the other hand, the two strands in duplex DNA become fully separated above a critical temperature, called the melting temperature. 76 These considerations are critical in our study since we have studied the binding and unzipping kinetics for both the nucleic acids under physiological realistic conditions (310K temperature, 150 mM NaCl concentration) separately. Such conditions resemble the intercellular region of a human cell and can alter the stability of a nucleic acid – SWCNT hybrid formed at a physiologically less stringent condition. A comparatively higher magnitude of duplex unzipping and in addition weakening of nucleic acid – CNT interaction at some of the above conditions would be more relevant in the context of gene delivery where complete unzipping of the RNA followed by its detachment from the carrier is anticipated upon the cellular uptake of the hybrid. 77 We have presented the data of simulations at six different conditions in Figure 6 for two reasons. First, we want to ascertain the condition where the nucleic acid – CNT binding is optimal and hence the duplex unzipping is most feasible. Second, we want to see whether the propensity of nucleobase stacking to SWCNT followed by unwinding of the duplex chain is more favourable for XNA than RNA at any given simulation conditions in this study or not. This second objective is based on our understanding that if an artificially synthesized XNA is to be preferred for gene delivery over a naturally occurring RNA, the former should fulfil the above requirements better at any given simulation condition.

(a)

(b)

14 (c)

ACS Paragon Plus Environment

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FIG.7. (a) Time evolution of the number of close contacts of XNA / DNA within a distance cut-off of 5 Å from the SWCNT (b) the free energy of XNA / RNA - CNT binding as a function of the separation between their COMs and (c) the variation of the number of inter – chain WC hydrogen bonds in XNA / RNA with time at various simulation conditions (different combinations of NaCl concentration and temperature of the medium).

Figure 7a indicates that a comparatively higher number of contact formation within a specified distance cut-off for any of the nucleic acids is observed when both the NaCl concentration as well as the temperature is low (black and red lines, Figure 7a). This trend is reversed when higher number of counterions is around reducing Nc for both XNA (green line) and RNA (violet line) at the same temperature. However, the highest number of contacts is formed between the SWCNT and either XNA (blue line) or RNA (pink line) when the simulations are carried out at a higher temperature (310K). It is to be noted further that at any given simulation condition XNA makes higher number of close contacts with the SWCNT as compared to that of RNA. Similar insights can be drawn from Figure 7b which estimates the contact pair minima in the qualitative free energy profile for XNA – CNT binding to be -9.136±0.091 and -7.426±0.087 kJ/mol both at 300K temperature but at two different salt concentrations (black and green curves respectively, Figure 7b). However, the XNACNT binding turns out to be the strongest at 310K temperature implied by the highest magnitude of free energy of binding (-10.157±0.014 kJ/mol) between the above two species (blue line, Figure 7b) which is much more negative in magnitude than the free energy of RNA-CNT binding (-7.803±0.183 kJ/mol) at the above condition (pink line, Figure 7b). Similarly, the RNA - CNT free energy of binding curves exhibit much lower depth of the contact pair minima as compared to that of XNA at other simulation conditions (red and violet curves, Figure 7b) as well. We would like to reiterate again that the estimations of binding free energies in Figure 7b does not involve the sampling of exact equilibrium states and are qualitative at their best. The different degrees of interactions of the nucleic acids with the SWCNT at various simulation conditions are also manifested in the persistence of the duplex WC hydrogen bonds as a function of the simulation time. Figure 7c signals at the higher extent of duplex chain unwinding in XNA as compared to that of RNA at identical simulation conditions. We observe that the XNA molecule is almost completely unzipped at a temperature of 310K (blue line, Figure 7c) whereas a significant number of inter – strand WC hydrogen bonds survives when either the simulation temperature is lower (black line) or the ionic strength of the medium is higher (green line). An increased temperature of the system seems congenial to the faster unzipping of the nucleic acids since thermal fluctuations tend to destabilize the hydrogen bonds in a duplex nucleic acid.

78

Another plausible reason may be an enhanced depletion of the aqueous layer between the

hydrophobic CNT and the hydrophilic nucleic acids at a higher temperature which facilitates the binding of the above two species and thus fastening the duplex unwinding process. On the contrary, an increased salt concentration helps the nucleic acid attain a more compact state with a higher stretch modulus due to the reduced phosphate – phosphate repulsion in the backbone.

27

Consequently, the 15



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Page 16 of 23

nucleic acid bases exhibit their unwillingness to participate in binding with the CNT which results in a slower unzipping of the duplex. Figure 7c once again confirms the faster rate of XNA unzipping compared to RNA at any of the above simulation conditions.

IV. CONCLUSIONS

In this paper, using atomistic MD simulations we address some important physiological factors controlling the unzipping of a novel double stranded xylonucleic acid (XNA) assisted by a rigid single – walled carbon nanotube without chemical degradation. The xylonucleic acid composed of xylose sugar units is a stereoisomer of a naturally occurring RNA having identical arrangements of nucleobases. Unlike the RNA, XNA adopts an extended helical geometry with a severely strained phosphate backbone. Such artificially synthesized RNA analogues are alien to the RNA – specific enzymes and thus are less easily degraded inside human body. This makes XNA a promising candidate for specific gene delivery

79, 80

and treatment of RNA viruses that trigger cancer.

33

However, such potential applications of these substrates are limited by the feasibility of the duplex chain unwinding mediated by a suitable carrier to yield two separate nucleotides which can bind with the mRNA and hinder the corresponding gene expression at physiological conditions. 28 In our study, the non-functionalized SWCNT plays the role of a transfecting carrier of XNA and it attempts to mimic the functionality of RISC induced siRNA duplex unzipping during a typical RNAi technique. 29, 31

Our simulations show that the unzipping is faster for XNA than that of RNA at identical

simulation conditions which is presumably due to the non-planar arrangements of nucleobases in XNA that reduce the stability of the WC hydrogen bonds when compared with that of RNA having higher lifetimes of WC hydrogen bonds. Furthermore, the consideration of temperature and salt concentration in probing the stability of SWCNT – nucleic acid hybrids is imperative to us since at higher salt concentration, the screening of the negative ionic charges make them less efficient for binding as compared to the charge neutral case causing slower unzipping while the thermal fluctuations at relatively higher temperature seem to be more helpful in duplex unwinding. We carry out simulations at 35 and 150 mM concentrations of salt separately since the ionic environment in the intra and the extracellular regions are different and it may affect the unzipping of the nucleic acid significantly. In order to extrapolate further physiological relevance to an ideal cellular environment we perform additional simulations at 310K showing that XNA undergoes almost complete unzipping while the corresponding RNA is partially unzipped at this temperature. To the best of our knowledge, this is the first computational study that demonstrates the interactions between an artificial duplex RNA analogue and a single wall carbon nanotube on a molecular level at various physiological conditions. It is to be noted that the current study involves the use of pristine carbon nanotubes


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without taking into account its inherent toxicity which can however be minimized by proper functional modification of the CNT.

81, 82

Nevertheless, Our study deals with a thermally and

enzymatically more robust RNA alternative having prospects in various applications ranging from antisense therapy to biomedicines. It is to be noted further that longitudinal motion, particularly motion in the axis perpendicular to the SWCNT surface, could also be indicative of nucleic acid instability on the SWCNT due to a relatively weaker π-π stacking interaction leading to a higher dissociation rates for nucleobases. Future studies in this direction will include the penetration of the cell membrane by XNA – CNT hybrids and the determination of the driving force detaching the two species in a cellular environment at a later stage.

Supporting Information Available: Radial distribution functions, g(r) between XNA/RNA and SWCNT COMs, and brief overview of each of the simulated systems. This material is available free of charge via the Internet at http://pubs.acs.org”.

Author Information Corresponding Author *

Email: [email protected]

Mailing Address: IIT Bombay, Department of Chemistry, Mumbai-400076, India Phone: + 91-022-2576 7192. Fax : + 91-022-2576 7152.

Disclosure Statement

The authors declare no competing financial interest.

ACKNOWLEDGEMENTS R.C thanks SERB (SB/SI/PC-55/2013), CSIR (Project No. 01(2781)/14/EMR-II) and IIT BombayIRCC (Grant number: 12IRCCSG046) for funding. S.G thanks CSIR, Govt. of India, for a senior research fellowship.



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REFERENCES

1

Ramaswamy, A.; Froeyen, M.; Hardewijn, P.; Ceulemans, A. Helical Structure of Xylose-DNA. J. Am. Chem.

Soc. 2010, 132, 587 – 595. 2

Nielsen, P. E. Peptide Nucleic Acids and the Origin of Life. Chem. BiodiVers. 2007, 4, 1996–2002.

3

Wengel, J.; Petersen, M.; Frieden, M.; Koch, T. Chemistry of Locked Nucleic Acids (LNA): Design,

Synthesis, and Bio-Physical Properties. Lett. Pept. Sci. 2004, 10, 237–253. 4

Egli, M.; Pallan, P. S. Insights from Crystallographic Studies into the Structural and Pairing Properties of

Nucleic Acid Analogs and Chemically Modified DNA and RNA Oligonucleotides. Annu. ReV. Biophys. Biomol. Struct. 2007, 36, 281– 305. 5

Lescrinier, E.; Esnouf, R.; Schraml, J.; Busson, R.; Heus, H. A.; Hilbers, C. W.; Herdewijn, P. Solution

Structure of a HNA – RNA Hybrid. Chem. Biol. 2000, 7, 719–731. 6

Meggers, E.; Zhang, L. Synthesis and Properties of the Simplified Nucleic Acid Glycol Nucleic Acid. Acc.

Chem. Res. 2010, 43, 1092 – 1102. 7

Lagriffoule, P.; Wittung, P.; Eriksson, M.; Jensen, K. J.; Norden, B.; Buchardt, O.; Nielsen, P. E. Peptide

Nucleic Acids with a Conformationally Constrained Chiral Cyclohexyl-Derived Backbone. Chem. Eur. J. 1997, 3, 912 – 919. 8

Kalota, A.; Karabon, L.; Swider, C. R.; Viazovkina, E.; Elzagheid, M.; Damha, M. J.; Gewirtz, A. M. 2′-

Deoxy-2′-Fluoro-β-D -Arabinonucleic Acid (2′F-ANA) Modified Oligonucleotides (ON) Effect Highly Efficient, and Persistent, Gene Silencing. Nucleic Acids Res. 2006, 34, 451 – 461. 9

Heuberger, B. D.; Switzer, C. Nonenzymatic Oligomerization of RNA by TNA Templates. Org. Lett. 2006, 8,

5809–5811. 10

Marliere,P. The Farther, the Safer: A Manifesto for Securely Navigating Synthetic Species away from the Old

Living World. Syst. Synth.Biol.. 2009, 3, 77–84. 11

Yu, H.; Zhang, S.; Chaput, J. C. Darwinian Evolution of an Alternative Genetic System Provides Support for TNA

as an RNA Progenitor. Nat. Chem. 2012, 4, 183–187. 12

Wang, Q.; Chen, Li.; Long, Y.; Tian, H.; Wu, J. Molecular Beacons of Xeno-Nucleic Acid for Detecting

Nucleic Acid. Theranostics 2013, 3, 395 – 408. 13

Taylor, A. T.; Pinheiro, V. B.; Smola, M. J.; Morgunov, A. S.; Chew, S.P.; Cozens, C.; Weeks, K. M.;

Hardejwin, P.; Holliger, P. Catalysts from Synthetic Genetic Polymers. Nature 2015, 518, 427 – 430. 14

Maiti, M.; Maiti, M.; Knies, C.; Dumbre, S.; Lescrinier, E.; Rosemeyer, H.; Ceulemans, A.; Hardewijn, P.

Xylonucleic acid: Synthesis, Structure, and Orthogonal Pairing Properties. Nucleic Acids Res. 2015, 43, 7189 – 7200.


Page 19 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


15

Liu, Z.; Winters, M.; Holodniy, M.; Dai, H. J. siRNA Delivery into Human T Cells and Primary Cells with

Carbon-Nanotube Transporters. Angew. Chem. Int. Ed. 2007, 46, 2023 – 2017. 16

Liu, Z.; Tabakman, S.; Welsher, K.; Dai, H. J. Carbon Nanotubes in Biology and Medicine: In vitro and in

vivo Detection, Imaging and Drug Delivery. Nano Res. 2009, 2, 85 – 120. 17

Zheng, M.; Jagota, A.; Semke, E.D.; Diner, B.A.; McLean, R.S.; Lustig, S.R.; Richardson, R.E.; Tassi, N.G.

DNA-Assisted Dispersion and Separation of Carbon Nanotubes. Nat. Mater. 2003, 2, 338–342. 18

Dovbeshko, G.I.; Repnytska, O.P.; Obraztsova, E.D.; Shotgun, Y.M. DNA Interaction with Single-Walled

Carbon Nanotubes: A SEIRA Study. Chem. Phys. Lett. 2003, 372, 432–437. 19

Ito, M.; Kobayashi, T.; Ito, Y.; Hayashida, T.; Nii, D.; Umemura, K.; Homma, Y. Intense Photoluminescence

from Dried Double-Stranded DNA and Single-Walled Carbon Nanotube. Appl. Phys. Lett. 2014, 104, 043102(1) – 043102(3). 20

Manohar, S.; Tang, T.; Jagota, A. Structure of Homopolymer DNA-CNT Hybrids. J. Phys. Chem. C 2007,

111, 17835-17845. 21

Lau, E. Y.; Lightstone, F. C.; Colvin, M. E. Dynamics of DNA Encapsulated in a Hydrophobic Nanotube.

Chem. Phys. Lett. 2005, 412, 82 – 87. 22

Cheng, C. L.; Zhao, G. Steered Molecular Dynamic Simulation Study on Dynamic Self-Assembly of Single-

Stranded DNA with Double-Walled Carbon Nanotube and Graphene. Nanoscale 2012, 4, 2301–2305. 23

Nandy, B.; Santosh, M.; Maiti, P. K. Interaction of Nucleic Acids with Carbon Nanotubes and Dendrimers. J.

Biosci. 2012, 37, 457 – 474. 24

Roxbury, D.; Jagota, A.; Mittal, J. Sequence-Specific Self-Stitching Motifs of Short Single-Stranded DNA on

a Single-Walled Carbon Nanaotube. J. Am. Chem. Soc. 2011, 133, 13545–13550. 25

Terry, C. A.; Fernandez, M.; Gude, L.; Lorente, A.; Grant, K. B. Physiologically Relevant Concentrations of

NaCl and KCl Increase Photocleavage by an N-Substituted 9-Aminomethylanthracene Dye. Biochemistry 2011, 50, 10375−10389. 26

Li, Y.; Lu, J.; Han, Y.; Fan, X.; Ding, S. RNA Interference Functions as an Antiviral Immunity Mechanism in

Mammals. Science 2013, 342, 231 – 234. 27

Santosh, M.; Panigrahi, S.; Bhattacharyya, D.; Sood, A. K.; Maiti, P. K. Unzipping and Binding of Small

Interfering RNA with Single Walled Carbon Nanotube: A Platform for Small Interfering RNA Delivery. J. Chem. Phys. 2012, 136, 065106 (1 – 10). 28

Ghidiyal, M.; Zamore, P. D. Small Silencing RNAs: an Expanding Universe. Nat. Rev. Genet. 2009, 10, 94 –

108. 29

Zamore, P. D.; Haley, B. Ribo-gnome: The Big World of Small RNAs. Science 2005, 309, 1519 – 1524.

30

Meister, G.; Tuschl, T. Mechanisms of Gene Silencing by Double-Stranded RNA. Nature 2004, 431, 238 –

243. 31

Lu, Q.; Moore, J. M.; Huang, g.; Mount, A. S.; Rao, A. M.; Larcom, L. L.; Ke, P. C. RNA Polymer

Translocation with Single-Walled Carbon Nanotubes. Nano Lett. 2004, 4, 2473 – 2477. 32

Elmén, J.; Thonberg, H.; Ljungberg, K.; Frieden, M.; Westergaard, M.; Xu, Y.; Wahren, B.; Liang, Z.; Ørum,

H.; Koch, T et al. Locked nucleic acid (LNA) Mediated Improvements in siRNA Stability and Functionality. Nucl. Acids Res. 2005, 33, 439 – 447.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

33

Page 20 of 23

Appella, D. H. Non-Natural Nucleic Acids for Synthetic Biology. Curr. Opin. Chem. Biol. 2009, 13, 687 –

696. 34

Bumcrot, D.; Manoharan, M.; Koteliansky, V.; Shah, D. W. Y. RNAi Therapeutics: A Potential New Class of

Pharmaceutical Drugs. Nat. Chem. Biol. 2006, 2, 711 – 719. 35

Jacque, J. M.; Triques, K.; Stevenson, M. Modulation of HIV-1 Replication by RNA Interference. Nature

2002, 418, 435 – 438. 36

Hess, B.; Kutzner, C.; van der Spoel.; Lindahl, D, E. GROMACS 4: Algorithms for Highly Efficient, Load-

Balanced, and Scalable Molecular Simulation. J. Chem. Theory. Comput. 2008, 4, 435-447. 37

Denning, E. J.; Priyakumar, U. D.; Nilsson, L.; MacKerell, Jr. A. D. Impact of 2'-Hydroxyl Sampling on the

Conformational Properties of RNA: Update of the CHARMM All-Atom Additive Force Field for RNA. J. Chem. Theory. Comput. 2011, 32, 1929 - 1943. 38

Berman, H.M.; Westbrook, J. ; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne ,

P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242. 39

Zou, J.; Ji, B. H.; Feng, X. Q.; Gao, H. J. Self-Assembly of Single-Walled Carbon Nanotubes into

Multiwalled Carbon Nanotubes in Water: Molecular Dynamics Simulations. Nano Lett. 2006, 6, 430−434. 40

Price, D. J.; Brooks III, C. L. A Modified TIP3P Water Potential for Simulation with Ewald Summations. J.

Chem. Phys. 2004, 121, 10096-10103. 41

Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graph. 1996, 14, 33-38.

42

Zhao, X. C.; Johnson, J. K. Simulation of Adsorption of DNA on Carbon Nanotubes. J. Am. Chem. Soc. 2007,

129, 10438– 10445. 43

Lacerda, L.; Raffa, S.; Prato, M.; Kostarelos, K. Cell-Penetrating CNTs for Drug Delivery of Therapeutics.

Nanotoday 2007, 2, 38-43. 44

Petrova, S. S.; Solev’ev, A. D. The Orgin of the Method of Steepest Descent. Historia Mathematica 1997, 24,

361-375. 45

Parrinello, M.; Rahman, A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method.

J. Appl. Phys. 1981, 52, 7182-7190. 46

G. Bussi, D. Donadio, M. Parrinello. Canonical Sampling through Velocity Rescaling. J. Chem. Phys. 2007,

126, 014101(1) – 014101(7). 47

Feller, S. E.; Zhang, Y.; Pastor, R.W.; Brooks, B. R. Constant Pressure Molecular Dynamic Simulation: The

Langevin Piston Method. J. Chem. Phys. 1995, 103, 4613-4621. 48

Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquid; Oxford University Press: Clarendon, U.K.;

1987. 49

Anderson, H. C. Rattle: A ‘Velocity’ Version of the Shake Algorithm for Molecular Dynamics Calculations. J.

Comp. Phys. 1983, 52, 24-32. 50

Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N-log(N) Method for Ewald Sums in Large

Systems. J. Chem. Phys. 1993, 98, 10089-10092.


Page 21 of 23

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


51

Martin, W.; Zhu, W.; Krilov, G. Simulation Study of Noncovalent Hybridization of Carbon Nanotubes by

Single-Stranded DNA in Water. J. Phys. Chem. B 2008, 112, 16076 – 16089. 52

Xiao, Z.; Wang, X.; Xu, X.; Zhang, H.; Li, Y.; Wang, Y. Base and Structure-Dependent DNA Dinucleotide-

Carbon Nanotube Interactions: Molecular Dynamics Simulations and Thermodynamic Analysis. J. Phys. Chem. C 2011, 115, 21546–21558. 53

Ghosh, S.; Patel, N.; Chakrabarti, R. Probing the Salt Concentration Dependent Nucleobase Distributions in a

Single-Stranded DNA – Single Walled Carbon Nanotube Hybrid. J. Phys. Chem. B 2016, 120, 455 – 466. 54

Alegret, N.; Santos, E.; Rodriguez-Fortea, A.; Rius, F. X.; Poblet, J. M. Disruption of Small Double Stranded

DNA Molecules on Carbon Nanotubes: A Molecular Dynamics Study. Chem. Phys. Lett. 2012, 525, 120 – 124. 55

Lu, G.; Maragakis, P.; Kaxiras, E. Carbon Nanotube Interaction with DNA. Nano Lett. 2005, 5, 897 – 900.

56

Zhao, Z.; Liu, Y.; Yan, H. DNA Origami Templated Self-Assembly of Discrete Length Single Wall Carbon

Nanotubes. Org. Biomol. Chem. 2013, 11, 596 – 598. 57

Illiafar, S.; Mittal, J.; Vezenov, D.; Jagota, A. Interaction of Single-Stranded DNA with Curved Carbon

Nanotube is Much Stronger than with Flat Graphite. J. Am. Chem. Soc. 2014, 136, 12947 – 12957. 58

Priyakumar, U. D.; Mackerell, A. D. Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative

Study of the Performance of Nucleic Acid Force Fields, CHARMM, AMBER and BMS. J. Chem. Theory. Comput. 2006, 2, 187-200. 59

Norberg, J.; Nilsson, L. Stacking Free Energy Profiles for All 16 Natural Ribodinucleoside Monophosphates

in Aqueous Solutions. J. Am. Chem. Soc. 1995, 117, 10832-10840. 60

Schöppe, A.; Hinz, H.J.; Rosemeyer, H.; Seela, F. Xylose-DNA: Comparison of the Thermodynamic Stability

of Oligo(2′-Deoxyxylonucleotide) and Oligo(2′-Deoxyribonucleotide) Duplexes. Eur. J. Biochem. 1996, 239, 33 – 41. 61

Poopeiko, N. E.; Juhl, M.; Vester, B.; SØrensen, M. D.; Wengel, J. Xylo-Configured Oligonucleotides (XNA,

Xylo Nucleic Acid): Synthesis of Conformationally Restricted Derivatives and Hybridization Towards DNA and RNA Complements. Bioorg. Med. Chem. Lett. 2003, 13, 2285–2290. 62

Lomzov, A. A.; Vorobjev, Y. N.; Pyshnyi, D. V. Evaluation of the Gibbs Free Energy Changes and Melting

Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation. J. Phys. Chem. B 2015, 119, 15221−15234. 63

Shiraki, T.; Tsuzuki, A.; Toshimitsu, F.; Nakashima, N. Thermodynamics for the Formation of Double –

Stranded DNA – Single – Walled Carbon Nanotube Hybrids. Chem. Eur. J. 2016, 22, 4774 – 4779. 64

Mogurampelly, S.; Panigrahi, S.; Bhattacharyya, D.; Sood, A. K.; Maiti, P. K. Unravelling siRNA Unzipping

Kinetics with Graphene. J. Chem. Phys. 2012, 137, 054903(1) – 054903(9). 65

Eriksson, M. A.; Nilsson, L. Structure, Thermodynamics and Cooperativity of the Glucocorticoid Receptor

DNA-Binding Domain in Complex with Different Response Elements, Molecular Dynamics Simulation and Free Energy Perturbation Studies. J. Mol. Biol. 1995, 253, 453-472. 66

Torrie, G. M.; Valleau, J. P. Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation -

Umbrella Sampling. J. Comput. Phys. 1977, 23, 187 – 199. 67

Tomari, Y.; Matranga, C.; Haley, B.; Martinez, M.; Zamore, P. D. A Protein Sensor for siRNA Asymmetry.

Science 2004, 306, 1377 – 1380. 68

Luzar, A. Resolving the Hydrogen Bond Dynamics Conundrum. J. Chem. Phys. 2000, 113, 10663-10675.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

69

Page 22 of 23

Kumar, N.; Kishore, N. Mechanistic Insights into Osmolyte Action in Protein Stabilization under Harsh

Conditions: N-Methylacetamide in Glycine Betaine-Urea Mixture. Chem. Phys. 2014, 443, 133-141. 70

Wang, F.; Wu, Y.; Tan, Z. Salt Contribution to the Flexibility of Single-Stranded Nucleic Acid of Finite

Length. Biopolymers 2012, 99, 370-381. 71

Ghosh, S.; Dixit, H.; Chakrabarti, R. Ion Assisted Structural Collapse of a Single Stranded DNA: A Molecular

Dynamics Approach. Chem. Phys. 2015, 459, 137-147. 72

Jorgensen, W. L.; Pranata, J. Importance of Secondary Interactions in Triply Hydrogen Bonded Complexes:

Guanine-Cytosine vs Uracil - 2, 6-Diaminopyridine. J. Am. Chem. Soc. 1990, 112, 2008 – 2010. 73

Tinoco, I.; Bustamante. C. How RNA Folds. J. Mol. Biol. 1999, 293, 271–281.

74

Bloomfield, V. A. DNA Condensation by Multivalent Cations. Biopolymers 1997, 44, 269–282.

75

Tan, Z.; Chen, S. Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and

Chain Length. Biophysical J. 2006, 90, 1175 – 1190. 76

Schildkraut, C.; Lifson, S. Dependence of the Melting Temperature of DNA on Salt Concentration.

Biopolymers 1965, 3, 195 – 208. 77

Bianco, A.; Kostarelos, K.; Prato, M. Applications of Carbon Nanotubes in Drug Delivery. Curr. Opin. Chem.

Biol. 2005, 9, 674–679. 78

Blake, R. D.; Delcourt, S. G. Thermal Stability of DNA. Nucleic Acids Res. 1998, 26, 3323 – 3332.

79

Pinheiro, V. B.; Holliger, P. Towards XNA Nanotechnology: New Materials from Synthetic Genetic

Polymers. Trends Biotechnol. 2014, 32, 321 – 328. 80

Singh, R.; Pantarotto, D.; McCarthy, D.; Chaloin, O.; Hoebeke, J.; Partidos, C. D.; Briand, J.; Prato, M.;

Bianco, A.; Kostarelos, K. Binding and Condensation of Plasmid DNA onto Functionalized Carbon Nanotubes: Toward the Construction of Nanotube-Based Gene Delivery Vectors. J. Am. Chem. Soc. 2005, 127, 4388-4396. 81

Lam. C. W.; James, J. T.; McCluskey, R.; Hunter, R. L. Pulmonary Toxicity of Single-Wall Carbon

Nanotubes in Mice 7 and 90 Days after Intratracheal Instillation. Toxicol. Sci. 2004, 77, 126 – 134. 82

Cui, D. X.; Tian, F. R.; Ozkan, C. S.; Wang, M.; Gao, H. J. Effect of Single Wall Carbon Nanotubes on

Human HEK293 Cells. Toxicol. Lett. 2005, 155, 73 – 85.


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TOC 434x184mm (96 x 96 DPI)


Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single

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