Irreversible denaturation of DNA: a method to precisely control the optical and thermo-optic properties of DNA thin solid films
The denaturation of double-stranded deoxyribonucleic acid (ds-DNA) has been well known to break nucleobase bonds, resulting in single-stranded deoxyribonucleic acid (ss-DNA) in solutions, which can recombine to form ds-DNA in a reversible manner. We developed an efficient process to irreversibly maintain various DNA denaturation levels in thin solid films in order to investigate the impacts of the denaturation on the optical properties of DNA films. By adding NaOH in an aqueous solution of salmon testis DNA, we flexibly controlled the level of denaturation in the solution, which was then spin-coated on Si and silica substrates to irreversibly bind ss-DNAs in a thin solid film. The denaturation of DNA in thin solid films was experimentally confirmed by ultraviolet-visible and Fourier transform infrared spectroscopic investigations, whose level could be controlled by the NaOH content in the aqueous solution precursor. By this irreversible denaturation process, we developed a new method to flexibly vary the refractive index of DNA thin solid films in a wide range of Δn>0.02 in the visible to near-infrared range. Thermo-optic coefficients dn/dT of the films were also experimentally measured in the temperature range from 40°C to 90°C to confirm the significant impacts of denaturation. Detailed thin film processes and optical characterizations are discussed.
基金项目：National Research Foundation of Korea (NRF)10.13039/501100003725 (2016k1A3A1A09918616).
Paulson Bjorn：Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
Seongjin Hong：Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
Seunguk Cheon：Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
Kyunghwan Oh：Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 120-749, South Korea
【1】J. D. Watson, and F. H. Crick, “A structure for deoxyribose nucleic acid,” Nature 171 , 737–738 (1953).
【2】B. Singh, N. S. Sariciftci, J. G. Grote, and F. K. Hopkins, “Bio-organic-semiconductor-field-effect-transistor based on deoxyribonucleic acid gate dielectric,” J. Appl. Phys. 100 , 024514 (2006).
【3】J. A. Hagen, W. Li, A. Steckl, and J. Grote, “Enhanced emission efficiency in organic light-emitting diodes using deoxyribonucleic acid complex as an electron blocking layer,” Appl. Phys. Lett. 88 , 171109 (2006).
【4】A. Steckl, H. Spaeth, H. You, E. Gomez, and J. Grote, “DNA as an optical material,” Opt. Photon. News 22 , 34–39 (2011).
【5】Y. Kawabe, L. Wang, S. Horinouchi, and N. Ogata, “Amplified spontaneous emission from fluorescent dye doped DNA-surfactant complex films,” Adv. Mater. 12 , 1281–1283 (2000).
【6】E. M. Heckman, R. S. Aga, A. T. Rossbach, B. A. Telek, C. M. Bartsch, and J. G. Grote, “DNA biopolymer conductive cladding for polymer electro-optic waveguide modulators,” Appl. Phys. Lett. 98 , 103304 (2011).
【7】R. Khazaeinezhad, S. H. Kassani, B. Paulson, H. Jeong, J. Gwak, F. Rotermund, D.-I. Yeom, and K. Oh, “Ultrafast nonlinear optical properties of thin-solid DNA film and their application as a saturable absorber in femtosecond mode-locked fiber laser,” Sci. Rep. 7 , 41480 (2017).
【8】A. Kulkarni, B. Kim, S. R. Dugasani, P. Joshirao, J. A. Kim, C. Vyas, V. Manchanda, T. Kim, and S. H. Park, “A novel nanometric DNA thin film as a sensor for alpha radiation,” Sci. Rep. 3 , 2062 (2013).
【9】S. Hong, W. Jung, T. Nazari, S. Song, T. Kim, C. Quan, and K. Oh, “Thermo-optic characteristic of DNA thin solid film and its application as a biocompatible optical fiber temperature sensor,” Opt. Lett. 42 , 1943–1945 (2017).
【10】W. Jung, H. Jun, S. Hong, B. Paulson, Y. S. Nam, and K. Oh, “Cationic lipid binding control in DNA based biopolymer and its impacts on optical and thermo-optic properties of thin solid films,” Opt. Mater. Express 7 , 3796–3808 (2017).
【11】E. Hebda, M. Jancia, F. Kajzar, J. Niziol, J. Pielichowski, I. Rau, and A. Tane, “Optical properties of thin films of DNA-CTMA and DNA-CTMA doped with Nile blue,” Mol. Cryst. Liq. Cryst. 556 , 309–316 (2012).
【12】B. Paulson, I. Shin, H. Jeong, B. Kong, R. Khazaeinezhad, S. R. Dugasani, W. Jung, B. Joo, H.-Y. Lee, and S. Park, “Optical dispersion control in surfactant-free DNA thin films by vitamin B2 doping,” Sci. Rep. 8 , 9358 (2018).
【13】J. Marmur, and P. Doty, “Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature,” J. Mol. Biol. 5 , 109–118 (1962).
【14】J. Marmur, and P. Ts’o, “Denaturation of deoxyribonucleic acid by formamide,” Biochim. Biophys. Acta 51 , 32–36 (1961).
【15】M.-S. Hung, and Y.-T. Huang, “Laser-induced heating for cell release and cellular DNA denaturation in a microfluidics,” BioChip J. 7 , 319–324 (2013).
【16】J. G. Wetmur, and N. Davidson, “Kinetics of renaturation of DNA,” J. Mol. Biol. 31 , 349–370 (1968).
【17】H. R. Massie, and B. H. Zimm, “Kinetics of denaturation of DNA,” Biopolymers 7 , 475–493 (1969).
【18】M. Ageno, E. Dore, and C. Frontali, “The alkaline denaturation of DNA,” Biophys. J. 9 , 1281–1311 (1969).
【19】P. Ehrlich, and P. Doty, “The alkaline denaturation of deoxyribose nucleic acid,” J. Am. Chem. Soc. 80 , 4251–4255 (1958).
【20】F. W. Studier, “Sedimentation studies of the size and shape of DNA,” J. Mol. Biol. 11 , 373–390 (1965).
【21】X. Wang, H. J. Lim, and A. Son, “Characterization of denaturation and renaturation of DNA for DNA hybridization,” Environ. Health Toxicol. 29 , e2014007 (2014).
【22】C. L. Schildkraut, J. Marmur, and P. Doty, “The formation of hybrid DNA molecules and their use in studies of DNA homologies,” J. Mol. Biol. 3 , 595–617 (1961).
【23】P. Doty, J. Marmur, J. Eigner, and C. Schildkraut, “Strand separation and specific recombination in deoxyribonucleic acids: physical chemical studies,” Proc. Natl. Acad. Sci. USA 46 , 461–476 (1960).
【24】A. Samoc, A. Miniewicz, M. Samoc, and J. G. Grote, “Refractive index anisotropy and optical dispersion in films of deoxyribonucleic acid,” J. Appl. Polym. Sci. 105 , 236–245 (2007).
【25】J. Nizio?, K. Maky?a-Juzak, M. M. Marzec, R. Ekiert, M. Marzec, and E. Gondek, “Thermal stability of the solid DNA as a novel optical material,” Opt. Mater. 66 , 344–350 (2017).
【26】S. Sun, D. Thompson, U. Schmidt, D. Graham, and G. J. Leggett, “Micro-/nano-patterning of DNA and rapid readout with SERS tags,” Chem. Commun. 46 , 5292–5294 (2010).
【27】T. Masuda, A. Yamaguchi, M. Hayashida, F. Asari-Oi, S. Matsuo, and H. Misawa, “Visualization of DNA hybridization on gold thin film by utilizing the resistance effect of DNA monolayer,” Sens. Actuators B 105 , 556–561 (2005).
【28】Y.-W. Kwon, C. H. Lee, D.-H. Choi, and J.-I. Jin, “Materials science of DNA,” J. Mater. Chem. 19 , 1353–1380 (2009).
【29】P. Y. Vadimovich, “UV absorbance of aqueous DNA,” Eur. J. Biophys. 3 , 19–22 (2015).
【30】P. Doty, H. Boedtker, J. Fresco, R. Haselkorn, and M. Litt, “Secondary structure in ribonucleic acids,” Proc. Natl. Acad. Sci. USA 45 , 482–499 (1959).
【31】B. Gnapareddy, S. R. Dugasani, T. Ha, B. Paulson, T. Hwang, T. Kim, J. H. Kim, K. Oh, and S. H. Park, “Chemical and physical characteristics of doxorubicin hydrochloride drug-doped salmon DNA thin films,” Sci. Rep. 5 , 12722 (2015).
【32】G. Tyagi, D. K. Jangir, P. Singh, and R. Mehrotra, “DNA interaction studies of an anticancer plant alkaloid, vincristine, using Fourier transform infrared spectroscopy,” DNA Cell Biol. 29 , 693–699 (2010).
【33】X. Wang, and A. Son, “Effects of pretreatment on the denaturation and fragmentation of genomic DNA for DNA hybridization,” Environ. Sci. Process. Impacts 15 , 2204–2212 (2013).
【34】L. Wang, J. Yoshida, N. Ogata, S. Sasaki, and T. Kajiyama, “Self-assembled supramolecular films derived from marine deoxyribonucleic acid (DNA)–cationic surfactant complexes: large-scale preparation and optical and thermal properties,” Chem. Mater. 13 , 1273–1281 (2001).
【35】S. Elhadj, G. Singh, and R. F. Saraf, “Optical properties of an immobilized DNA monolayer from 255 to 700??nm,” Langmuir 20 , 5539–5543 (2004).
【36】K. Oh, and U.-C. Paek, Silica Optical Fiber Technology for Devices and Components: Design, Fabrication, and International Standards (Wiley, 2012).
【37】T. Eggeman, “Sodium Hydroxide ,” in Kirk-Othmer Encyclopedia of Chemical Technology (Wiley, 2011).
【38】A. L. Olsen, and E. R. Washburn, “An interpolation table for refractive index-normality relationship for solutions of hydrochloric acid and sodium hydroxide,” Trans. Kans. Acad. Sci. 40 , 117–126 (1937).
【39】Z. Zhang, P. Zhao, P. Lin, and F. Sun, “Thermo-optic coefficients of polymers for optical waveguide applications,” Polymer 47 , 4893–4896 (2006).
Hayoung Jeong, Paulson Bjorn, Seongjin Hong, Seunguk Cheon, and Kyunghwan Oh, "Irreversible denaturation of DNA: a method to precisely control the optical and thermo-optic properties of DNA thin solid films," Photonics Research 6(9), 918-924 (2018)