Лахно В.Д., Винников А.В.
Молекулярные устройства на основе ДНК
Математическая биология и биоинформатика. 2021;16(1):115-135.
doi: 10.17537/2021.16.115.
Список литературы
- Dragon A. Polymerase chain reaction. Sci. Am. 1998;278(5):112. doi: 10.1038/scientificamerican0598-112
- Winfree E., Liu F., Wenzler L.A., Seeman N.C. Design and self-assembly of two-dimensional DNA crystals. Nature. 1998;394(6693):539–544. doi: 10.1038/28998
- Seeman N.C. Nanotechnology and the double helix. Sci. Am. 2004;290(6). doi: 10.1038/scientificamerican0604-64
- Wang M.D., Yin H., Landick R., Gelles J., Block S.M. Stretching DNA with optical tweezers. Biophyz. J. 1997;72(3):1335–1346. doi: 10.1016/S0006-3495(97)78780-0
- Bustamante C., Keller D.J. Scanning Force Microscopy. Biology Physics Today. 1995;48:32. doi: 10.1063/1.881478
- Strick T.R., Allemand J.-F., Bensimon D., Bensimon A., Croguette V. The elasticity of a single supercoiled DNA molecule. Science. 1996;271(5257):1835–1837. doi: 10.1126/science.271.5257.1835
- Bockelmanan U., Essevaz-Roulet B., Heslot F. DNA strand separation studied by single molecule force measurements. Phys. Rev. E. 1998;58:2386. doi: 10.1103/PhysRevE.58.2386
- Braun E., Eichen Y., Sivan U., Ben-Yoseph G. DNA-templated assembly and electrode attachment of a conducting silver wire. Nature. 1998;391:775–778. doi: 10.1038/35826
- Eley D.D., Spivey D.I. Semiconductivity of organic substances. Part 9. Nucleic acid in the dry state. Trans. Faraday Soc. 1962;58:411–415. doi: 10.1039/TF9625800411
- Roth S.R. One-Dimensional Metals, 1st ed. Weinheim :VCH, 1995:31–35.
- Warman J.M., de Haas M. P., Rupprecht A DNA: a molecular wire? Chem. Phys. Lett. 1996;249:319–322. doi: 10.1016/0009-2614(95)01429-2
- Introduction to radiobiology. Eds. Dutreix J., Wambersie A., Tubiana M. London: CRC Press, 1990.
- Frenkel K. Carcinogen-mediated oxidant formation and oxidative DNA damage. Pharmacol. Ther. 1992;53:127–166. doi: 10.1016/0163-7258(92)90047-4
- Ames B.N., Shigenaga M.K., Hagen T.M. Oxidants, antioxidants, and the degenerative diseases of aging. Proc. Natl. Acad. Sci. USA. 1993;90:7915–7922. doi: 10.1073/pnas.90.17.7915
- Loft S., Poulsen H.E. Cancer risk and oxidative DNA damage in man. J. Mol. Med. 1996;74:297–312. doi: 10.1007/BF00207507
- Gros. F. Colloque “Risques cancérogènes dus aux rayonnements ionisants” 14–16 mai 1998. In: Comptes Rendus De l'Academie Des Sciences. Serie III, Sciences De La Vie. Eds. Cros F., Tubiana M., Sarasin A., Masse R., Maustacchi E., Früry-Herrard A., Rosa J. 1999;322(2–3):87–88. doi: 10.1016/S0764-4469(99)80028-6
- O’Neill P., Fielden E.M. 2 - Primary Free Radical Processes in DNA. Advances in Radiation Biology. 1993;17:53. doi: 10.1016/B978-0-12-035417-7.50005-2
- Retel J., Hoebee B., Braun J.E.F., Lutgernik J.T., Akker E., Handayani Wanamarta A., Joenje H., Lafleur M.V.M. Mutational specificity of oxidative DNA damage. Mutations Res. 1993;299:165–182. doi: 10.1016/0165-1218(93)90094-T
- Demple B., Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu. Rev. Biochem. 1994;63:915–948. doi: 10.1146/annurev.bi.63.070194.004411
- Turro N.J., Barton J.K. Paradigms, supermolecules, electron transfer and chemistry at a distance. What's the problem? The science or the paradigm? J. Biol. Inorg. Chem. 1998;3:201–209. doi: 10.1007/s007750050222
- Lewis F.D., Wu T., Liu X. , R.L. Letsinger, S.R. Greenfield, S.E. Miller, M.R. Wasielewski. Dynamics of Photoinduced Charge Separation and Charge Recombination in Synthetic DNA Hairpins with Stilbenedicarboxamide Linkers. J. Am. Chem. Soc. 2000;122(12):2889–2902. doi: 10.1021/ja993689k
- Murphy C.J., Arkin M.A., Jenkins Y., Ghatlia N.D., Bossmann S.H., Turro N.J., Barton J.K. Long-range photoinduced electron transfer through a DNA helix. Science. 1993;262:1025–1029. doi: 10.1126/science.7802858
- Hall D.B., Holmlin R.E., Barton J.K. Oxidative DNA damage through long-range electron transfer. Nature. 1996;382:731–735. doi: 10.1038/382731a0
- Kelley S.O., Jackson N.M., Hall M.G., Barton J.K. Long Range Electron Transfer through DNA Films. Angew. Chem. Int. Ed. 1999;38:941–945. doi: 10.1002/(SICI)1521-3773(19990401)38:7<941::AID-ANIE941>3.0.CO;2-7
- Brun A.M., Harriman A. J. Dynamics of electron transfer between intercalated polycyclic molecules: effect of interspersed bases. J. Am. Chem. Soc. 1992;114:3656–3660. doi: 10.1021/ja00036a013
- Mead T.J., Kayem J.F. Electron Transfer through DNA: Site-Specific Modification of Duplex DNA with Ruthenium Donors and Acceptors. Angew. Chem. Int. Ed. Engl. 1995;34:352–354. doi: 10.1002/anie.199503521
- Draganescu A., Tullius T.D. Targeting of nucleic acids by iron complexes. Metal Ions in Biological Systems. 1996;33:453–484.
- Brun A.M., Harriman A. Energy- and electron-transfer processes involving paladium phorphyrins bound to DNA. J. Am. Chem. Soc. 1994;116:10383–10393. doi: 10.1021/ja00102a004
- Harriman A. Electron Tunneling in DNA. Angew. Chem. Int. Ed. 1999;38:945–949. doi: 10.1002/(SICI)1521-3773(19990401)38:7<945::AID-ANIE945>3.0.CO;2-S
- Lincoln P., Tuite E., Norden B. Short-Circuiting the Molecular Wire: Cooperative Binding of Δ-[Ru(phen)2dppz]2+ and Δ-[Rh(phi)2bipy]3+ to DNA. J. Am. Chem. Soc. 1997;119:1454-1455. doi: 10.1021/ja9631965
- Olson E. J.C., Hu D., Hörmann A., Barlbara P.F. Quantitative Modeling of DNA-Mediated Electron Transfer between Metallointercalators. J. Phys. Chem. B. 1997;101:299–303. doi: 10.1021/jp963109v
- Lewis F. D., Letsinger R.L Distance-dependent photoinduced electron transfer in synthetic single-strand and hairpin DNA. J. Biol. Inorg. Chem. 1998;3:215–221. doi: 10.1007/s007750050224
- Krider E.S., Mead T.J. Electron transfer in DNA: covalent attachment of spectroscopically unique donor and acceptor complexes. J. Biol. Inorg. Chem. 1998;3:222–225. doi: 10.1007/s007750050225
- Boon E.M., Barton J.K Charge transport in DNA. Curr. Opin. Stuct. Biol. 2002;12:320–329. doi: 10.1016/S0959-440X(02)00327-5
- Henderson P.T., Jonnes D., Hampikin G., Kan Y., Schuster G.B. Long-distance charge transport in duplex DNA: the phonon-assisted polaron-like hopping mechanism. Proc. Nat. Acad. Sci. USA. 1999;96:8353–8358. doi: 10.1073/pnas.96.15.8353
- Lewis F.D., Wu T., Zhang Y., Letsinger R.L., Greenfeld S.R., Wasielewski M.R. Distance-dependent electron transfer in DNA hairpins. Science. 1997;277:673–676. doi: 10.1126/science.277.5326.673
- Meggers E., Michel-Beyerle M.E., Giese B. Sequence Dependent Long Range Hole Transport in DNA. J. Am. Chem. Soc. 1998;120:12950–12955. doi: 10.1021/ja983092p
- Giese B., Wessely S., Spormann M., Lindeman U., Meggers E., Michel-Begerle M.E. On the Mechanism of Long Range Electron Transfer through DNA. Angew. Chem. Int. Ed. 1999;38:996–998. doi: 10.1002/(SICI)1521-3773(19990401)38:7<996::AID-ANIE996>3.0.CO;2-4
- Bixon M., Giese B., Wessly S., Langenbacher. T., Michel-Beyerle M.E., Jortner J. Long-range charge hopping in DNA. PNAS. 1999;96:11713–11716. doi: 10.1073/pnas.96.21.11713
- Giese B., Amaudrut J., Köhler A.K., Spormann M., Wessely S. Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling. Nature. 2001;412:318–320. doi: 10.1038/35085542
- Giese B. Long-distance charge transport in DNA: the hopping mechanism. Acc. Chem. Res. 2000;33:631–636. doi: 10.1021/ar990040b
- Porath D, Bezryadin A., de Vries S., Dekker C. Direct measurement of electrical transport through DNA molecules. Nature. 2000;403:635–638. doi: 10.1038/35001029
- Fink H.W., Schönenberger C. Electrical conduction through DNA molecules. Nature. 1999;398:407–410. doi: 10.1038/18855
- Kasumov A.Y., Kociak M., Gueron S., Reulet B., Volkov V.T., Klinov D.V., Bouchiat H. Proximity-induced superconductivity in DNA. Science. 2001;291:280–282. doi: 10.1126/science.291.5502.280
- Watanabe H., Manabe C., Shigematsu T., Shimotani K., Shimizu M. Single molecule DNA device measured with triple-probe atomic force microscope. Appl. Phys. Lett. 2001;79:2462–2464. doi: 10.1063/1.1408604
- Shigematsu T., Shimotani K., Manabe C., Watanabe H., Shimizu M. Transport properties of carrier-injected DNA. J. Chem. Phys. 2003;118:4245–4252. doi: 10.1063/1.1541608
- Storm A.J., van Noort J., de Vries S., Dekker C. Insulating behavior for DNA molecules between nanoelectrodes at the 100 nm length scale. Appl. Phys. Lett. 2001;79:3881–3883. doi: 10.1063/1.1421086
- Cai I., Tabata H., Kawai T. Self-assembled DNA networks and their electrical conductivity. Appl. Phys. Lett. 2000;77:3105–3106. doi: 10.1063/1.1323546
- Lee H.Y., Tanaka H., Otsuka Y., Yoo K.H., Lee J., Kawai T. Control of electrical conduction in DNA using oxygen hole doping. Appl. Phys. Lett. 2002;80:1670. doi: 10.1063/1.1456972
- Tabata H., Cai L.T., Gu J.H., Tanaka S., Otsuka Y., Sacho Y., Taniguchi M., Kawai T. Toward the DNA electronics. Sinth. Met. 2003;133:469–472. doi: 10.1016/S0379-6779(02)00386-7
- Rakitin A., Aich P., Papadopoulos C., Kobzar Y., Vedeneev A.S., Lee J.S., Xu J.M. Metallic Conduction through Engineered DNA: DNA Nanoelectronic Building Blocks. Phys. Rev. Lett. 2001;86:3670–3673. doi: 10.1103/PhysRevLett.86.3670
- Aich P., Labiuk S.L., Tari L.W., Delbaere L.J.T., Roesler W.J., Falk K.J., Steer R.P., Lee J.S. M-DNA: A complex between divalent metal ions and DNA which behaves as a molecular wire. J. Mol. Biol. 1999;294:477–485. doi: 10.1006/jmbi.1999.3234
- Wetting S.D., Wood D.O., Lee J.S. Thermodynamic investigation of M-DNA: a novel metal ion–DNA complex. Journal of Inorganic Biochemistry. 2003;94:94–99. doi: 10.1016/S0162-0134(02)00624-4
- Li C.Z., Long Y.T., Kraatz H.B., Lee J.S. Electrochemical Investigations of M-DNA Self-Assembled Monolayers on Gold Electrodes. J. Phys. Chem. B. 2003;107:2291–2296. doi: 10.1021/jp026792w
- Yoo K.H., Ha D.H., Lee J.O., Park J.W., Kim J., J.J. Kim, H.-Y. Lee, T. Kawai, Han Yong Choi. Electrical conduction through poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA molecules. Phys. Rev. Lett. 2001;87:198102. doi: 10.1103/PhysRevLett.87.198102
- Okahata Y., Kobayashi T., Tanaka K., Shimomura M. Anisotropic Electric Conductivity in an Aligned DNA Cast Film. J. Am. Chem. Soc. 1998;120:6165–6166. doi: 10.1021/ja980165w
- Braun E., Eichen Y., Sivan U., Ben-Yoseph G. DNA-templated assembly and electrode attachment of a conducting silver wire. Nature. 1998;391:775–778. doi: 10.1038/35826
- Gu Q., Cheng C., Gonela R., Suryanarayanan S., Anabathula S., Dai K., Haynie D.T. DNA nanowire fabrication. Nanotechnology. 2006;17:R14–R25. doi: 10.1088/0957-4484/17/1/R02
- Lee J.S., Latimer J.P., Reid R.S. A cooperative conformational change in duplex DNA induced by Zn2+ and other divalent metal ions. Biochem. Cell. Biol. 1993;71:162–168. doi: 10.1139/o93-026
- Lee S.W., Mao C., Flynn C.E., Belcher A.M. Ordering of quantum dots using genetically engineered viruses. Science. 2002;296:892–895. doi: 10.1126/science.1068054
- Flynn C.E., Lee S.W., Peelle B.R., Belcher A.M. Viruses as vehicles for growth, organization and assembly of materials. Acta Materialia. 2003;51:5867–5880. doi: 10.1016/j.actamat.2003.08.031
- Yoo P.J., Nam K.T., Qi J., Lee S.-K., Park J., Belcher A.M., Hammond P.T. Spontaneous assembly of viruses on multilayered polymer surfaces. Nature Materials. 2006;5:234–240. doi: 10.1038/nmat1596
- Nam K.T., Kim D.-W., Yoo P.J., Chiang C.-Y., Meethong N., Hammond P.T., Chiang Y.-M., Belcher A.M. Virus-Enabled Synthesis and Assembly of Nanowires for Lithium Ion Battery Electrodes. Science. 2006;316:885–888. doi: 10.1126/science.1122716
- Frontiers in Biochip Technology. Eds. Dr. Wan-Li Xing, Dr. Jing Cheng. Springer, 2006. 358 p.
- Microarrays: Volume I: Synthesis Methods. Ed. Jang B. Rampal. Humana Press, 2007. 452 p. (Methods in Molecular Biology; Vol. 381).
- Marchand G., Delattre C., Campagnolo R., Pouteau P., Ginot F. Electrical detection of DNA hybridization based on enzymatic accumulation confined in nanodroplets. Analytical Chem. 2005;77:5189–5195. doi: 10.1021/ac0505066
- Gooding J.J. Electrochemical DNA hybridization biosensors. Electroanalysis. 2002;14:1149–1156. doi: 10.1002/1521-4109(200209)14:17<1149::AID-ELAN1149>3.0.CO;2-8
- Palecek E., Jelen F. Electrochemistry of Nucleic Acids and Development of DNA Sensors. Crit. Rev. Anal. Chem. 2002;3:261–270. doi: 10.1080/10408340290765560
- Wang J. Electrochemical nucleic acid biosensors. Anal. Chim. Acta. 2002;469:63–71. doi: 10.1016/S0003-2670(01)01399-X
- Drummond T.G., Hill M.G., Barton J.K. Electrochemical DNA sensors. Nature Biotechnology. 2003;21:1192–1199. doi: 10.1038/nbt873
- Hahm J., Lieber C.M. Direct Ultrasensitive Electrical Detection of DNA and DNA Sequence Variations Using Nanowire Nanosensors. Nano Letters. 2004;4(1):51–54. doi: 10.1021/nl034853b
- Popovich N.D., Thorp H.H. New strategies for electrochemical nucleic acid detection. Interface. 2002;11:30–34. doi: 10.1149/2.F05024IF
- Demers L.M., Clinger D.S., Park S.-J, Li Z., Chung S.-W., Mirkin C.A. Direct Patterning of Modified Oligonucleotides on Metals and Insulators by Dip-Pen Nanolithography. Science. 2002;296:1836–1838. doi: 10.1126/science.1071480
- Ginger D.S., Zhang H., Mirkin C.A. The evolution of dip-pen nanolithography. Angewandte Chem. 2004;43:30–45. doi: 10.1002/anie.200300608
- Seeman N.C. An overview of structural DNA nanotechnology. Mol. Biotech. 2007;37:246–257. doi: 10.1007/s12033-007-0059-4
- Seeman N.C. From genes to machines: DNA nanomechanical devices. Trends Biochem. Sci. 2005;30:119-125. doi: 10.1016/j.tibs.2005.01.007
- Seeman N.C., Lukeman P.S. Nucleic acid nanostructures: bottom-up control of geometry on the nanoscale. Rep. Progr. Phys. 2005;68:237–270. doi: 10.1088/0034-4885/68/1/R05
- Lakhno V.D., Sultanov V.B. On the Possibility of Electronic DNA Nanobiochips. JCT. 2007:3. doi: 10.1021/ct6003438
- Luo Y., Collier C.P., Jeppesen J.O., Nielsen K.A., DeIonno E., Ho G., Perkins J., Tseng H.‐R., Yamamoto T., Stoddart J.F., Heath J.R. Two-dimensional molecular electronics circuits. Chem. Phys. Chem. 2002;3:519–525. doi: 10.1002/1439-7641(20020617)3:6<519::AID-CPHC519>3.0.CO;2-2
- Green J.E., Choi J.W., Boukai A., Bunimovich Y., Johnston-Halperin E., DeIonno E., Luo Y., Sheriff B.A., Xu K., Shik Shin Y., Tseng H.-R., Stoddart J.F., Heath J.R. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimeter. Nature. 2007;445:414–417. doi: 10.1038/nature05462
- Tseng R.J., Tsai C., Ma L., Onyang J., Ozkan C.S., Yang Y. Digital memory device based on tobacco mosaic virus conjugated with nanoparticles. Nature Nanotechnology. 2006;1:72–77. doi: 10.1038/nnano.2006.55
- Aviram A., Ratner M.A. Molecular Rectifiers. Chem. Phys. Lett. 1974;29:277–283. doi: 10.1016/0009-2614(74)85031-1
- Callier C.P., Wong E.W., Belobradsky M., Raymo F.M., Stoddart J.F., Kuekes P.J., Williams R.S., Heath J.R. Electronically configurable molecular-based logic gates. Science. 1999;285:391–394. doi: 10.1126/science.285.5426.391
- Zhou C., Deshpande M.R., Reed M.A.Nanoscale metal/self-assembled monolayer/metal heterostructures. Appl. Phys. Lett. 1997;71:611–613. doi: 10.1063/1.120195
- Porath D., Cuniberty G., Felice R.D. Charge Transport in DNA-Based Devices. Top. Curr. Chem. 2004;237:183–227. doi: 10.1007/b94477
- Lakhno V.D., Sultanov V.B. Electronic XOR logic gate based on DNA. Math. Biol. Bioinf. 2006;1:123. doi: 10.17537/2006.1.123
- Otsuka Y., Lee H.Y., Gu J.H., Lee J.-O., Yoo K.-H., Tanaka H., Tabata H., Kawai T. Influence of Humidity on the Electrical Conductivity of Synthesized DNA Film on Nanogap Electrode. Jpn. J. Appl. Phys. 2002;41:891–894. doi: 10.1143/JJAP.41.891
- Gu J.H., Cai L., Tanaka S., Otsuka Y., Tabata H., Kawai T. Electric conductivity of dye modified DNA films with and without light irradiation in various humidities. J. Appl. Phys. 2002;92:2816–2820. doi: 10.1063/1.1498959
- Taniguchi M., Lee H.Y., Tanaka H., Kawai T. Electrical Properties of Poly(dA)·Poly(dT) and Poly(dG)·Poly(dC) DNA Doped with Iodine Molecules. Jpn. J. Appl. Phys. 2003;42. L.215–L216. doi: 10.1143/JJAP.42.L215
- Goldhaber-Gordon D.J., Montemerlo M.S., Love J.C., Optiteck G.J., Ellenbogen J.C. Overview of nanoelectronic devices. IEEE. 1997;85(4):521–540. doi: 10.1109/5.573739
- Lent C.C., Tongaw P.D. A device architecture for computing with quantum dots. Proc. IEEE. 1997;85:542–557. doi: 10.1109/5.573740
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