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Optical Band Gap and Hall Transport Characteristics of Lanthanide Ion Modified DNA Crystals Sreekantha Reddy Dugasani, Taewoo Ha, Si Joon Kim, Bramaramba Gnapareddy, Sanghyun Yoo, Keun Woo Lee, Tae Soo Jung, Hyun Jae Kim, Sung Ha Park, and Jae Hoon Kim J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.5b03875 • Publication Date (Web): 29 May 2015 Downloaded from http://pubs.acs.org on May 30, 2015

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The Journal of Physical Chemistry

Optical Band Gap and Hall Transport Characteristics of Lanthanide Ion Modified DNA Crystals

Sreekantha Reddy Dugasani,† Taewoo Ha,§ Si Joon Kim,⊥ Bramaramba Gnapareddy,† Sanghyun Yoo,† Keun Woo Lee,† Tae Soo Jung,⊥ Hyun Jae Kim,⊥* Sung Ha Park,†* Jae Hoon Kim§*

†

Department of Physics and SKKU Advanced Institute of Nanotechnology (SAINT) Sungkyunkwan University, Suwon 440-746, Korea §

⊥

Department of Physics, Yonsei University, Seoul 120-749 Korea

School of Electrical and Electronic Engineering, Yonsei University, Seoul 120-749, Korea

*E-mail: [email protected] (HJK) *E-mail: [email protected] (JHK) *E-mail: [email protected] (SHP), Phone: +82-31-299-4544, Fax: +82-31-290-7055

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ABSTRACT: Lanthanide ion-modified DNA crystals are fabricated on quartz and silica substrates via surface-assisted growth, and the optical band gap and electrical Hall transport are measured at room temperature for these crystals. The optical band gap of these crystals show an increasing behaviour and the second band onset showed the inverted V shape upon increasing the lanthanide ion concentration. At a particular concentration of each lanthanide ion into the DNA crystals exhibited with low resistivity, low Hall mobility, high free carrier concentration, and a minimum magneto resistance. The experimental results show feasibility in controlling important physical parameters, such as the band gap energy and Hall parameters by adjusting the concentration of the lanthanide ion. When combined with the existing structural versatility of DNA nanostructures, these functional tunabilities will be crucial for the future development of DNA-based nanoelectronic and biophotonic devices.

Keywords: Self-assembly, Ion Doping, Optical Property, Hall Mobility


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INTRODUCTION DNA molecules have the capacity for bottom-up self-assembly, easy programmability, and effective biocompatibility and, as a result, can serve as building materials for nano-scale structures by providing control over the structural and chemical features of complex geometries at the molecular level. In the past few decades, a number of studies have determined that DNA-based self-assembly is one of the most predictable and reliable methods to achieve bottom-up construction. DNA has been used to obtain a wide range of artificially designed nanostructures with different shapes and patterns,1-6 which allows for the fabrication of properly functionalized DNA nanostructures. DNA can be functionalized with proteins, nanoparticles, nanowires, and metal ions,7-12 and this enables specific functionalities for new applications within a given area of interest while offering a facile route for design and fabrication of the DNA nanostructures through simple molecular modification. One such example involves ion modification of DNA molecules with trivalent lanthanide ions (Ln3+), but Ln3+ modified DNA (Ln3+-DNA) molecules have not yet been systematically investigated in terms of their various physical, chemical, and biological properties. Ln3+-DNA nanostructures have begun to attract attention because Ln3+ has distinct physical characteristics that make it a useful material in electromagnetic, photonic and even medical applications. Ln3+ can be incorporated into DNA in a fine-tuned manner by varying the concentration of Ln3+, [Ln3+] in order to alter the properties and provide new functionality to pristine DNA. Here, we discuss Ln3+-DNA complexes doped with trivalent Ln3+, i.e., dysprosium (Dy3+), erbium (Er3+), europium (Eu3+), gadolinium (Gd3+), neodymium (Nd3+), and terbium ions (Tb3+). Interestingly, these novel complexes can be used in biophotonics or nanoelectronics because these ions have excellent luminescence and offer distinct optical and electrical properties. Researchers have investigated the optical and electrical properties of single- and 3 ACS Paragon Plus Environment


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double-stranded DNA molecules mostly in solution phase, and in these cases, there have been certain difficulties to determine the conductivity and energy band gap of target DNA samples with precision due to the existence of buffer solution containing various chemicals and counterions. In addition, the electrical conductivity of DNA molecules has yet to be fully understood since previous articles have reported DNA to have either insulator,13 semiconductor,14,15 conductor,16 or superconductor17 characteristics in specific environments. To avoid the ambiguities resulting from the buffer effect, we used substrate-assisted growth (SAG) to grow DNA crystals directly on specific substrates (quartz for optical band gap and silica for Hall transport)18-22 in order to measure their properties in ambient environment. Transparent quartz exhibits fundamental absorption below 190 nm and transmits 90% of the light above 200 nm, thereby providing favourable conditions for the band gap analysis of DNA crystals because the DNA absorption wavelength is of around 260 nm. For the Hall measurements, we used silica (with a 200 nm thick SiO2 layer) to provide an insulating layer without leakage and an atomically flat surface. In this report, we discuss the room temperature optical band gap and Hall transport characteristics of Ln3+-doped DNA crystals by controlling the concentration of [Ln3+].

EXPERIMENTAL METHODS The O2 plasma treatment was carried out with an O2 plasma cleaner (Plasma Processing System, CUTE-1MP/R, Gyeonggi, Korea) to clean and modify the surfaces of the quartz/silica substrates. The O2 plasma cleaner was operated under the following conditions: 50 W of power, 5 × 10−2 Torr of base pressure, an oxygen flow rate of 45 SCCM, a working oxygen pressure of 7.8 × 10−1 Torr, and 10 min of plasma generation time for the quartz substrate and 5 min for silica. The functional groups – mainly the silanol (SiOH) group –


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changed the surface charges into negative and imbued the substrates with hydrophilic propensities. Synthetic oligonucleotides, purified via high performance liquid chromatography, were purchased from Bioneer (Daejeon, Korea). The complexes were formed by mixing a 1× TAE/Mg2+ (40 mM Tris base, 20 mM

acetic acid, 1 mM EDTA (pH 8.0), and 12.5 mM

magnesium acetate) buffer solution that contained an equimolar mixture of 8 different DX strands. For annealing, the O2 plasma treated quartz/silica substrates were inserted along with the DNA strands into an AXYGEN-tube with a total sample volume of 250 µL. These samples were then placed in a Styrofoam box with 2 L of boiled water and were allowed to cool from 95 to 25 °C over a period of 24 hours to facilitate the hybridization process. During annealing, the DX strands formed polycrystalline DX crystals on the given substrate, and consequently, these polycrystalline crystals achieved full coverage on the quartz/silica surface. The samples were prepared with a concentration of 50 nM, which is well above minimum concentration of 10 nM for quartz and 20 nM for silica that are needed to achieve full coverage on a given substrate, i.e., the saturation concentration. After the DX DNA crystals formed on the quartz/silica substrate, the appropriate amount of

1

M of

Dy(NO3)3.xH2O,

Er(NO3)3.5H2O,

Eu(NO3)3.5H2O,

Gd(NO3)3.6H2O,

Nd(NO3)3.6H2O, or Tb(NO3)3.6H2O (Sigma Aldrich) were added at various concentrations (0, 0.5, 1, 2 and 4 mM). Then, the samples were incubated at room temperature for 24 hours. For AFM imaging, a sample that was obtained via SAG was placed on a metal puck using instant glue. 30 µL 1× TAE/Mg2+ buffer were added onto the substrate and another 20 µL of 1× TAE/Mg2+ buffer were dispensed into the AFM tip (NP-S10, Veeco Inc., USA). The AFM images were obtained with a Multimode Nanoscope (Veeco Inc., USA) in the fluid tapping mode. The optical transmission in the near-infrared (NIR), visible (Vis.), and ultraviolet (UV) regions (3300 ~ 175 nm) were measured by using a Varian Cary 5G spectrophotometer. The 5 ACS Paragon Plus Environment


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spectrophotometer is equipped with two light sources: a deuterium arc lamp (NIR and Vis.) and a quartz W-halogen lamp (UV). Two detectors are employed, including a cooled PbS detector for the NIR region and a photomultiplier tube for the Vis. and UV regions. The spectrophotometer measures the frequency-dependent light intensity that passes either through vacuum or through the sample. The present investigation focused on the wavelength region from 1200 to 190 nm. The Hall measurements were carried out to obtain the free carrier concentration, Hall mobility, Hall resistivity, and magneto resistance of Ln3+-DNA crystals using the van der Pauw configuration (HMS-3000, Ecopia). The Ln3+-DNA samples were rinsed with deionized (DI) water, followed by softly blowing with nitrogen gas to remove residual chemicals on a Ln3+-DNA crystal surface. The metal contact was then defined by placing silver paste on the four corners of the Ln3+-DNA sample with a sample size of 5 × 5 mm2.

RESULTS AND DISCUSSION DNA double-crossover (DX) crystals doped with six different Ln3+ ions (= Dy3+, Er3+, Eu3+, Gd3+, Nd3+, and Tb3+) were fabricated on quartz/silica substrates via SAG. A unit DX tile was organized in two DX junctions, and two parallel duplexes were tied up. Two types of DX tiles were used to construct two-dimensional (2D) DNA crystals on the given substrate (Figure S1, Tables S1 and S2 in supporting information), and the details for the sample preparation are further described in the experimental section that provides the processes for DNA crystal growth on quartz/silica substrates. The SAG method was used to fabricate an extremely thin monolayer of DNA crystals that achieved full coverage of O2 plasma-treated substrates, and the DX unit building blocks were observed to have dimensions of 12 nm × 4 nm while the DX DNA crystals bound on the substrate presented a thickness of 0.6 ± 0.2 nm


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in dry condition.23 Typical AFM thickness profiles of pristine DNA and Ln3+-DNA crystals were shown in Figure S2 in supporting information.



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Figure 1. Schematic diagrams of (a) Ln3+-DNA crystal fabrication, (b) a DX crystal comprised with DX1 and DX2 tiles, (c) Ln3+ coordination sites in the DNA molecule, and (d, e) experimental setups for energy band gap and Hall transport measurements, respectively. AFM images of (f) 1 mM of [Dy3+] (Dy 1); (g) 1 mM of [Er3+] (Er 1); (h) 1 mM of [Eu3+] (Eu 1); (i) 1 mM of [Gd3+] (Gd 1); (j) 1 mM of [Nd3+] (Nd 1); and (k) 1 mM of [Tb3+] (Tb 1) into DX DNA crystals. The yellow dotted lines in the AFM images (scan size of 1 × 1 µm2) reveal the DX DNA crystal boundaries. The insets in all AFM images are noise-filtered images (scan size of 100 × 100 nm2) reconstructed via fast Fourier transform to show the periodicity of the DX unit tiles.

Figure 1a shows the fabrication process for the Ln3+-DNA crystals via SAG. 1× TAE/Mg2+ buffer (40 mM Tris acetate (pH 8.0), 1 mM EDTA, and 12.5 mM magnesium acetate) was used during annealing with a temperature controlled from 95 to 25 °C over a period of 24 hours. After the annealing process had been completed, each Ln3+ was separately added to a test tube containing DX crystals on the substrates, followed by incubation at room temperature for ion doping. Figures 1b and 1c show an illustration of a DX lattice with two DX tiles, and the appropriate Ln3+ coordination sites (between base-pairs and the phosphate backbone) in a DNA duplex. Figure 1d depicts the experimental procedure that used a light source and an analyzer to measure the energy band gap, and Figure 1e presents the Hall transport measurement with a Hall coordinate system (left) and an easily movable slide magnet and DNA sample chip (right). The appropriate coordination sites of the Ln3+ in the DNA molecules were likely to be intercalated between the base-pairs, binding with the phosphate backbones through a similar mechanism as that of divalent metal ions. Eichhorn et al. proposed that the binding sites of divalent metal ions in DNA molecules were the phosphate backbones that possessed negative charges and the heterocyclic bases that contain electron donor atoms.24 Binding metal ions 9 ACS Paragon Plus Environment


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into DNA has been differentiated from geometrically stable DNA helical structures. Previously, modified DNA molecules where Zn2+ and Cu2+ were intercalated between basepairs under different environmental conditions – wet and dry – had also been discussed.

25,26

Furthermore, artificially designed one to five Cu2+-mediated base-pairs of hydroxypyridone nucleobases were uniformly consolidated into the middle of the DNA duplexes in a solution phase.27 Ln3+ doping was carried out after forming the DX DNA crystals on the given substrate. If the DNA strands are added together with Ln3+ in a buffer solution at the very beginning, certain limitations would prohibit constructing proper Ln3+-DNA crystals due to the relatively higher [Ln3+] during the annealing process. We studied the structural stability of Ln3+-DNA crystals as a function of [Ln3+] to identify the maximum doping concentration (saturation concentration, Cs). Empirical data indicates that all [Ln3+] discussed in the present study had a

Cs at around 1 mM (data not shown). Up to this Cs, the Ln3+-DNA crystals were guaranteed to form periodic DX lattice structures. However, a concentration above Cs for Ln3+, resulted in Ln3+-DNA complexes that had not assembled properly and presented aggregated, amorphous structures. In order to fabricate Ln3+-DNA crystals without deformation, even at a slightly higher [Ln3+] than Cs, we adopted the after-doping procedure. The appropriate amount of Ln3+ was added after the completion of DNA hybridization on a given substrate, which could guarantee obtaining DX structures free of deformations. The fixed experimental conditions during annealing included: the duration of the annealing process, which was controlled with 2 L of boiled water in a Styrofoam box, the amount of DX DNA on a given substrate according to the size of the substrate (5 × 5 mm2), and the total sample volume (250 µL) in the test tube. Different amounts of [Ln3+] such as 0, 0.5, 1, 2, and 4 mM were used as control parameters for the optical band gap and Hall transport measurements. The typical AFM images shown in Figure 1f-k correspond to a Cs of 1 mM for [Dy3+], [Er3+], [Eu3+], [Gd3+], [Nd3+], and [Tb3+], 10 ACS Paragon Plus Environment

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which are marked as Dy 1, Er 1, Eu 1, Gd 1, Nd 1, and Tb 1, respectively. The yellow dotted lines in the AFM images indicate the DX crystal boundaries, and the insets in the bottom right show the noise-filtered 2D spectrum images constructed by using a fast Fourier transform. These 2D spectra clearly indicate the periodicity of the unit building block (DX), and the surface morphologies of the Ln3+-DNA crystals were similar to those of DX DNA crystals, even at a relatively higher [Ln3+] since the ion doping was carried out after the formation of the DX crystals.

Figure 2. The absorption coefficient (α) as a function of the photon energy (E) of various [Ln3+] into the DX DNA crystals, and the variation in α(E) with different [Ln3+] for (a) Dy3+DNA, (b) Er3+-DNA, (c) Eu3+-DNA, (d) Gd3+-DNA, (e) Nd3+-DNA, and (f) Tb3+-DNA crystals.

We carried out visible-ultraviolet (VUV) spectrophotometry at ambient temperature and pressure to obtain the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) and optical band gap of Ln3+-DNA crystals from the transmittance 11 ACS Paragon Plus Environment


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spectra. Figure 2a-f shows the variation in the absorption coefficient (α) as a function of the photon energy (E) of the Ln3+-DNA crystals at various [Ln3+]. A large linear background is obtained from the quartz substrate without DX crystals, and this background feature was subtracted from all of the measured spectra before the analysis in order to remove the background effect produced by the quartz substrates. The fundamental absorption bands associated with the optical band gap, which is represented as the π → π* electronic transition, indicate a superposition of the corresponding HOMO-LUMO transitions in the DNA basepairs. Another strong absorption band placed next to the fundamental absorption band located at the high-energy tail comes from the superposition of the second absorption bands of the individual DNA base-pairs located at around 6 eV.

Figure 3. Photon energy analysis as a function of [Ln3+] into the DX DNA crystals. The variations in the optical band gap and second band onset with different concentrations of (a) Dy3+, (b) Er3+, (c) Eu3+, (d) Gd3+, (e) Nd3+, and (f) Tb3+ into the DX DNA crystals.


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The optical band gap corresponding to the Ln3+-DNA crystals varies from 4.72 to 4.87 eV, depending on the presence of the various [Ln3+]. The pristine DNA crystals exhibit a clear optical band gap of 4.72 eV, and earlier studies have reported that the HOMO-LUMO transitions of the DNA molecules in the solid phase are positioned in an energy range from 4.3 to 4.5 eV.28-31 The slight differences in the optical band gaps were likely to be a result of the differences in the geometry, number of nucleotides, sample environment, and interfacial characteristics. Here, we assigned the energy of the local maximum obtained from the experimental data α(E), as shown in Figure 2, and we then analyzed the doping-dependent optical band gap of the Ln3+-DNA crystals with various [Ln3+], as shown in Figure 3a-f. The blue-shift in the optical band gap is a result of the doped ions that act as a screen for the existing interaction between the DNA base-pairs. Consequently, the optical characteristics of the base-pairs in the Ln3+-DNA crystals approach those of the gas phase. In contrast with the optical band gap shown in Figure 3a-f, we also present the onset energy of the second optical absorption band, which evolves with ion doping in a different fitting. Our observations indicate that this second band onset generally increased as [Ln3+] increased up to Cs and then decreased as [Ln3+] further increased. Since there was some uncertainty in locating the onsets from the low-energy side of the second band gap via linear fitting, they had to be taken into account to provide a reliable second band onset estimation. The optical band gap represents the minimum energy needed to form an exciton, i.e., an electron-hole pair, and the resulting two-body state is not yet able to participate in the transport process that requires free electron-hole pairs. In contrast, the onset energy of the second optical absorption band was likely higher than the optical energy band gap, and the exciton that were excited to this band could immediately undertake intraband transitions to the bottom of the conduction band, forming current-carrying states. This phenomena has been reported for semiconductors consisted of organic materials as well.32,33 The Hall transport of the Ln3+-DNA crystals was determined by taking electrical Hall 13 ACS Paragon Plus Environment


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measurements with van der Pauw geometry under a 0.51 T magnetic field (B) at room temperature. As shown in Figure 4, we measured the carrier concentration (N), Hall mobility (µ), Hall resistivity (ρ) and magneto resistance (σ) as a function of [Ln3+] in order to understand the mechanism behind the electrical transport through Ln3+-DNA crystals. The Ln3+-DNA crystals show an N on the order of 1013 ~ 1016 cm-3, depending on the different Ln3+ as well as the [Ln3+] at which the Hall measurements were performed. The N increased as [Ln3+] increased from 0 to 1 mM, up to Cs, and then decreased as the concentration increased further. Interestingly, µ showed the opposite behaviour as N, that is, the lowest µ occurred at Cs. µ was basically determined by the impurity scattering and crystal deformation introduced as a result of the Ln3+ doping.

Figure 4. Characteristics of Hall transport. (a) Carrier concentration (N), (b) Hall mobility (µ), (c) Hall resistivity (ρ), and (d) magneto resistance (σ) of Dy3+, Er3+, Eu3+, Gd3+, Nd3+, and 14 ACS Paragon Plus Environment

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Tb3+ into DX DNA crystals as a function of [Ln3+].

The Ln3+ was intercalated throughout the highly ordered π electron system of base-pair stacking and bond to phosphate backbone – with the inclusion of the electrically active dopants – which in turn affects the Hall parameters through chemical changes. In addition, Ln3+ might act as a replacement for the proton in imino group that generates the N-Ln3+ stretching. The difference in N changes more rapidly around Cs than the differences in µ and ρ, which means N is more sensitive than µ and ρ to [Ln3+]. N and µ exhibit more extreme behaviour in the Ln3+-DNA crystals at around Cs, which corresponds to the optimal occupation of Ln3+ at the proper sites in the DNA molecules. However a lower ρ was obtained at different [Ln3+] in DNA crystals instead of in Cs, which could be a result of the differences in atomic radius and electron affinity of the dopant ions. ρ is known to have an inversely proportional dependence to N and to the scattering time, which in turn are both dependent on [Ln3+]. Finally, we have evaluated the σ of the Ln3+-DNA crystals by taking Hall measurements with respect to variations in [Ln3+] at a fixed B of 0.51 T, as shown in Figure 4d. When B is applied perpendicular to the direction of the current, the σ of the Ln3+-DNA crystals decreases relative to the σ of crystals without B. Initially, the σ decreased with an increase in the [Ln3+] up to Cs, and then increased as [Ln3+] increased further. The minimum of the σ takes place at around Cs, which corresponds to the state of the minimum disorder in the orientation of the neighbouring magnetic moments, which means that they are formed as long chains that are ferromagnetically aligned. The origin of the σ in the Ln3+-DNA crystals might be the spinrelated scattering and spin-dependent tunnelling of carriers between the neighbouring Ln3+, and the behaviour of σ could be a result of the electrical transport in a magnetic disorder state that is directly related to the structural transition, spin splitting of the band states, and 15 ACS Paragon Plus Environment


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exchange interactions under the B that is applied.

CONCLUSIONS In conclusion, we have fabricated 2D Ln3+-DNA crystals with full coverage on the quartz and the silica substrates via SAG and have studied the optical band gap and electrical Hall transport at room temperature. The HOMO-LUMO band gap of the Ln3+-DNA crystals exhibited an increasing behaviour, and the second band onset showed the inverted V shape upon an increase in [Ln3+]. At approximately Cs for each of the Ln3+ into the DNA crystals, a highest conductance was exhibited with low resistivity, low Hall mobility, and a high free carrier concentration. This means that the Cs of the Ln3+-doped DNA crystals is a reliable optimum concentration for molecular electronic devices. The optical and electrical investigations of the Ln3+-DNA crystals can serve as effective means to control the optical band gap energy, free charge carrier concentration, and mobility. In combination with the existing structural versatility of the DNA nanostructures, these functional tunabilities will be crucial to future development of DNA-based nanoelectronic and biophotonic devices and sensors.


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ASSOCIATED CONTENT Supporting Information Available: Schematic diagram, sequence pool, sticky-ends of the DX tiles, and the AFM thickness profile of DNA crystals. This material is available free of charge via the internet at http://pubs.acs.org.

AUTHOR INFORMATION Corresponding Authors *E-mail: [email protected] (HJK) *E-mail: [email protected] (JHK) *E-mail: [email protected] (SHP)

Notes The authors declare no competing financial interest.

ACKNOWLEDGMENTS This work was supported by the National Research Foundation of Korea (NRF), (NRF2013R1A1A2061731) to SRD, (NRF-2011-0028819) to HJK, (NRF-2012M3A7B4049801, NRF-2014R1A2A1A11053213) to SHP, and (NRF-2012M3A7B4049802) to JHK, funded by the Ministry of Science, ICT & Future Planning (MSIP) and the Ministry of Education, Science and Technology (MEST) of the Korean government.



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