Hydrogen bonding and DNA: 66-year retrospective (briefly)

Keywords: Yu.P. Blagoi, DNA, hydrogen bond, hydration, mutation, proton transition, preopeness of DNA duplex

Abstract

Background: As Yu.P. Blagoi, the memory of who is dedicated to this work, once said: "The molecular structure of DNA — the famous double helix — is stabilized by water molecules and metal ions". The central, key interaction that determines both the double-helix structure of DNA and its functioning (the genetic code, replication, mutagenesis) is hydrogen-bonded interaction.

Objectives: Demonstration of the diverse manifestations of the hydrogen bond in the structure and functioning of DNA.

Materials and Methods: A computer simulation based on the density functional method was used.

Results: This paper identifies a wide range of hydrogen-bonded interactions that determine key aspects of both DNA structures and functional features related to heredity (replication, mutagenesis).

Conclusions: The preopeness of DNA base pairs with an embedded water molecule on the exterior hydrogen bond create more favorable conditions for proton transitions between bases along the central hydrogen bond. In this case, the hydrogen bonds of the bases to a lesser extent hinder the transition of the proton due to the smaller electrostatic repulsion (due to a larger distance) between them. Therefore, the preopened pairs are likely to form tautomeric forms of nucleic acid bases and to originate a probable mechanism for the formation of point mutations in DNA. At the same time, the central hydrogen bonds with the imino groups of bases in pairs remain intact.

Downloads

Download data is not yet available.

References

Blagoi YP. DNA interaction with biologically active substances (metal ions, dyes, drugs). Soros Educational Journal. 1998;10:18–24. Available from: https://web.archive.org/web/20061209031559/http://journal.issep.rssi.ru/articles/pdf/9810_018.pdf (in Russian)

Karachevtsev VO, Kosevich MV, Zhigalova NM. In memory of Professor Yuri P. Blagoi. Bіophysical bulletin. 2018;39(1):81–2. https://doi.org/10.26565/2075-3810-2018-39-07 (in Ukrainian)

Watson JD, Crick FHC. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature. 1953;171:737–8. https://doi.org/10.1038/171737a0

Chambers DA, editor. DNA: The Double Helix. Perspective and Prospective at 40 Years. Ann N Y Acad Sci. 1995;758:1–441. Available from: https://nyaspubs.onlinelibrary.wiley.com/toc/17496632/1995/758/1

Pearson H. Beyond the double helix. Nature. 2003;421:310–2. https://doi.org/10.1038/421310a

Gilbert W. Life after the helix. Nature. 2003;421:315–6. https://doi.org/10.1038/421315a

Dennis C, Campbell P. The eternal molecule. Nature. 2003;421:396. https://doi.org/10.1038/nature01396

Wilkins MHF, Stokes AR, Wilson HR. Molecular structure of nucleic acids: Molecular structure of deoxypentose nucleic acids. Nature. 1953;171:738–40. https://doi.org/10.1038/171738a0

Franklin RE, Gosling RG. Molecular configuration in sodium thymonucleate. Nature. 1953;171:740–41. https://doi.org/10.1038/171740a0

Olby R. Quiet debut for the double helix. Nature. 2003;421:402–5. https://doi.org/10.1038/nature01397

McCarty M. Discovering genes are made of DNA. Nature. 2003;421:406. https://doi.org/10.1038/nature01398

Maddox B. The double helix and the 'wronged heroine'. Nature. 2003;421:407–8. https://doi.org/10.1038/nature01399

Pääbo S. The mosaic that is our genome. Nature. 2003;421:409–12. https://doi.org/10.1038/nature01400

Chakravarti A., Little A. Nature, nurture and human disease. Nature. 2003;421:412–4. https://doi.org/10.1038/nature01401

Bell JI. The double helix in clinical practice. Nature. 2003;421:414–6. https://doi.org/10.1038/nature01402

Kemp M. The Mona Lisa of modern science. Nature. 2003;421:416–20. https://doi.org/10.1038/nature01403

Ball P. Portrait of a molecule. Nature. 2003;421(6921):421–2. https://doi.org/10.1038/nature01404

Bustamante C, Bryant Z, Smith SB. Ten years of tension: single-molecule DNA mechanics. Nature. 2003;421:423–7. https://doi.org/10.1038/nature01405

Seeman NC. DNA in a material world. Nature. 2003;421:427–31. https://doi.org/10.1038/nature01406

Alberts B. DNA replication and recombination. Nature. 2003;421:431–5. https://doi.org/10.1038/nature01407

Friedberg EC. DNA damage and repair. Nature. 2003;421:436–40. https://doi.org/10.1038/nature01408

Nossal GJV. The double helix and immunology. Nature. 2003;421:440–4. https://doi.org/10.1038/nature01409

Hood L, Galas D. The digital code of DNA. Nature. 2003;421:444–8. https://doi.org/10.1038/nature01410

Felsenfeld G, Groudine M. Controlling the double helix. Nature 2003;421:448–53. https://doi.org/10.1038/nature01411

Watson JD, Berry A. DNA: the Secret of Life. New York: Alfred A. Knopf; 2003. 446 p. ISBN: 0-375-41546-7.

Hovorun D. Gold anniversary of DNA double helix discovery. Biopolym Cell. 2003;19(3):209–10. https://doi.org/10.7124/bc.19.3 (in Ukrainian)

Blagoi YP, Galkin VL, Gladchenko GO, et al. Metallokompleksy nukleinovykh kislot v rastvorakh [Metal-containing complexes of nucleic acides in solutions]. Maleev V.Ya, editor. Kyiv: Naukova dumka; 1991. 270 p. ISBN 5-12-002499-0 (In Russian).

Jeffrey GA, Saenger W. Hydrogen Bonding in Biological Structures. Berlin: Springer-Verlag; 1991. 569 p. https://doi.org/10.1007/978-3-642-85135-3

Moore TS, Winmill TF, CLXXVII. — The state of amines in aqueous solution. J Chem Soc, Trans. 1912;101:1635–76. https://doi.org/10.1039/CT9120101635

Huggins ML. 50 Years of Hydrogen Bond Theory. Angew Chem Int Ed. 1971;10:141–52. https://doi.org/10.1002/anie.197101471

Latimer WM, Rodebush WH. Polarity and ionization from the standpoint of the Lewis theory of valence. J Am Chem Soc. 1920;42(7):1419–33. https://doi.org/10.1021/ja01452a015

Pauling L. The shared-electron chemical bond. PNAS. 1928;14(4):359–62. https://doi.org/10.1073/pnas.14.4.359

Nernst W. Verteilung eines Stoffes zwischen zwei Lösungsmitteln und zwischen Lösungsmittel und Dampfraum. Z Phys Chem. 1891;8(1):110–39. https://doi.org/10.1515/zpch-1891-0806 (in German)

Werner A. Über Haupt- und Nebenvalenzen und die Сonstitution der Ammoniumverbindungen. Justus Liebigs Annal Chem. 1902;322:261–97. https://doi.org/10.1002/jlac.19023220302 (in German)

Oddo G, Puxeddu E. Sui 5-azoeugenoli e la costituzione dei cosidetti o-ossiazocomposti. Gazz Chim Ital. 1906;36(II):1–48.

Pfeiffer P, Fischer Ph, Kuntner J, Monti P, Pros Z. Zur theorie der Farblacke, II. Justus Liebigs Annal Chem. 1913;398:137–96. https://doi.org/10.1002/jlac.19133980203

Yukhnevich G.V. Vodorodnaja svjaz' – chastnyj sluchaj gipervalentnoj svjazi M.A. Il'inskogo [Hydrogen bond is a particular case of hypervalent bond by M.A. Illinski]. Idlis GM, editor. Issledovanija po istorii fiziki i mehaniki [Studies in the history of physics and mechanics]. Moscow: Nauka; 2003. p. 220–36. ISBN: 5-02-002834-7 (in Russian).

Lewis GN. Valence and Structure of Atoms and Molecules. New York: The Chemical Catalog Company, Inc.: 1923. 172 p.

Pimentel GC, McClellan AL. The Hydrogen Bond. Moscow: Mir; 1964. 462 p. (in Russian).

International Union of Pure and Applied Chemistry. Compendium of Chemical Terminology, Gold Book, Version 2.3.3, 2014-02-24. Available from: http://goldbook.iupac.org/files/pdf/goldbook.pdf

Arunan E, Desiraju GR, Klein RA, Sadlej J, Scheiner S, Alkorta I, et al. Definition of the hydrogen bond (IUPAC Recommendations 2011). Pure Appl Chem. 2011;83(8):1637–41. https://doi.org/10.1351/PAC-REC-10-01-02

Arunan E, Desiraju GR, Klein RA, Sadlej J, Scheiner S, Alkorta I, et al. Defining the hydrogen bond: An account (IUPAC Technical Report). Pure Appl Chem. 2011;83:1619–36. https://doi.org/10.1351/PAC-REP-10-01-01

Kryachko ES. The concept of protonation in examples: From atoms and molecules to Watson-Crick base pairs of DNA. In: Germogen A, editor. Protonation: properties, applications and effects. New York: Nova Science Publishers; 2019. p. 143–236. ISBN: 978-1-53614-886-2

Pauling L. The nature of the chemical bond and the structure of molecules and crystals: An introduction to modern structural chemistry. 3rd ed. New York: Cornell University Press; 1960. 644 p. ISBN-13: 978-0801403330

Kaplan I.G. Vvedenie v teoriiu mezhmolekuliarnykh vzaimodeistvii. [Introduction to the theory of intermolecular interactions]. Moscow: Nauka; 1982. 312 p. (in Russian)

Kryachko ES. Neutral blue-shifting and blue-shifted hydrogen bonds. In: Grabowski S, editor. Hydrogen Bonding — New Insights. Dordrecht: Springer; 2006. p. 293–336. https://doi.org/10.1007/978-1-4020-4853-1_8

Frank-Kamenetckii MD. Samaia glavnaia molekula [The most important molecule]. Moscow: Nauka; 1983. 160 p. (in Russian).

Sinden RR. DNA twists and flips. Nature. 2005;437:1097–8. https://doi.org/10.1038/4371097a

Volkov SN. The conformational dependence of low-frequency vibrations of DNA macromolecule. Biopolym Cell. 1991;7(1):40–9. https://doi.org/10.7124/bc.0002B0 (in Russian)

Watson JD, Crick FHC. The structure of DNA. Cold Spring Harb Symp Quant Biol. 1953;18:123–31. https://doi.org/10.1101/SQB.1953.018.01.020

Cochran W, Crick FHC, Vand V. The structure of synthetic polypeptides. I. The transform of atoms on a helix. Acta Cryst. 1952;5:581–6. https://doi.org/10.1107/S0365110X52001635

Wilkins MHF, Wilson HR, Hamilton LD. Secondary structure of DNA. PNAS. 1970;65(3):761–2. https://doi.org/10.1073/pnas.65.3.761

Wu TT. Secondary structures of DNA. PNAS. 1969;63(2):400–5. https://doi.org/10.1073/pnas.63.2.400

Watson JD. The Double Helix. A Personal Account of the Discovery of the Structure of DNA. New York: Atheneum; 1968. 226 p.

Asimov A. Geneticheskii kod [The Genetic Code]. Moscow: Tcentropoligraf; 2006. 202 p. (in Russian). ISBN: 5-9524-2230-6

Elkin LO. Rosalind Franklin and the Double Helix. Physics Today. 2003;56(3):42–8. https://doi.org/10.1063/1.1570771

Manchester KL. Did a tragic accident delay the discovery of the double helical structure of DNA? Trends Biochem Sci. 1995;20(3):126–8. https://doi.org/10.1016/s0968-0004(00)88981-1

Kuhn TS. Struktura nauchnykh revoliutcii [The structure of scientific revolutions]. Moscow: Progress; 1977. 300 p. (in Russian).

Dufour F. The Realities of 'Reality' — Part II: Making Sense of Why Modern Science Advances (Volume 1). 2018. Chapter XI: The Molecular Biology Revolution; p. 204–18. Available from: https://ssrn.com/abstract=3251682

Hoshika S, Leal NA, Kim M-J, Kim M-S, Karalkar NB, Kim H-J, et al. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science. 2019;363:884–7. https://doi.org/10.1126/science.aat0971

Warren M. Four new DNA letters double life’s alphabet. Nature. 2019;566:436. https://doi.org/10.1038/d41586-019-00650-8

Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NGJ. Structural basis for a six nucleotide genetic alphabet. J Am Chem Soc. 2015;137(21):6947–55. https://doi.org/10.1021/jacs.5b03482

Kryachko ES. The origin of spontaneous point mutations in DNA via Löwdin mechanism of proton tunneling in DNA base pairs: Cure with covalent base pairing. Int J Quantum Chem. 2002;90(2):910–23. https://doi.org/10.1002/qua.975

Jeffrey GA. An Introduction to Hydrogen Bonding. New York: Oxford University Press; 1997. 320 p. ISBN 0-19-509549-9

Saenger W. The Principles of Nucleic Acid Structure. Мoscow: Мir; 1987. 584 p. (in Russian).

Sinden RR. DNA Structure and Function. Academic Press: San Diego; 1994. 398 p. ISBN: 9780126457506

Bulavin LA, Hovorun DM, Nikolaienko TYu. Structure of the monomers of DNA. Кyiv: Naukova Dumka; 2014. 205 p. https://doi.org/10.13140/2.1.2257.1208 (in Russian)

Sukhodub LF. Interactions and hydration of nucleic acid bases in a vacuum. Experimental study. Chem Rev. 1987;87(3):589–606. https://doi.org/10.1021/cr00079a006

Gorb L, Podolyan Y, Dziekonski P, Sokalski WA, Leszczynski J. Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study. J Am Chem Soc. 2004;126(32):10119–29. https://doi.org/10.1021/ja049155n

Kryachko ES, Volkov SN. To the understanding of the mechanism of formation of point mutations in DNA. Dopov Nac acad nauk Ukr. 2018;7:103–12. https://doi.org/10.15407/dopovidi2018.07.103 (in Ukrainian).

Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian 09, Revision C.01; Gaussian, Inc.: Wallingford CT, 2010. Available from: https://gaussian.com/

Hoogsteen K. The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Cryst. 1963;16:907–16. https://doi.org/10.1107/S0365110X63002437

Nikolova EN, Kim E, Wise AA, O'Brien PJ, Andricioaei I, Al-Hashimi HM. Transient Hoogsteen base pairs in canonical duplex DNA. Nature. 2011;470:498–502. https://doi.org/10.1038/nature09775

Frank-Kamenetskii MD. DNA breathes Hoogsteen. Artificial DNA: PNA & XNA. 2011;2(1):1–3. https://doi.org/10.4161/adna.2.1.15509

Subirana JA. DNA discoveries through crystallography. Nature. 2003;423(6941):683. https://doi.org/10.1038/423683b

Nikolova EN, Zhou H, Gottardo FL, Alvey HS, Kimsey IJ, Al-Hashimi HM. A historical account of Hoogsteen base-pairs in duplex DNA. Biopolymers. 2013;99:955–68. https://doi.org/10.1002/bip.22334

Ichas M. Biologicheskii kod [Biological code]. Moscow: Mir. 1971. 352 p. (in Russian)

Six thousand pet dogs help find mutation for one breed's striking blue eyes. Nature. 2018;562:310. https://doi.org/10.1038/d41586-018-06987-w

Deane-Coe PE, Chu ET, Slavney A, Boyko AR, Sams AJ. Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies, PLoS Genet. 2018;14(10), e1007648. https://doi.org/10.1371/journal.pgen.1007648

Lehninger AL. Biochemistry: The Molecular Basis of Cells Structure and Function. Moscow: Mir; 1976. 960 p. (in Russian).

Stent GS, Kjelindar R. Molekuliarnaia genetika [Molecular genetics]. Moscow: Mir; 1974. 614 p. (in Russian).

Korzhinskii S. Geterogenesis i evolyutsiya. K teorii proishozhdeniya vidov [Heterogenesis and evolution. On theory of the origin of species]. Mémoires de l'Académie Impériale des Sciences de St. Pétersbourg. Série VIII. 1899;9(2):1–94. Available from: http://libarch.nmu.org.ua/bitstream/handle/GenofondUA/7317/4150d1dd5615e1288e0666d6427c6a47.djvu?sequence=1&isAllowed=y (in Russian).

Friz E. Molekuliarnyi mekhanizm mutatcii [Molecular mechanism of mutations] In: Belozerskii AN, editor. Molekuliarnaia genetika [Molecular genetics]. Part I. Moscow: Mir; 1964. p. 226–91. (in Russian)

De Friz G. Izbrannye proizvedeniia [Selected works]. Moscow: Gosudarstvennoe medicinskoe izdatel'stvo; 1932. 148 р. (in Russian). ISBN: 978-5-4458-1972-1

Chetverikov SS. O nekotorykh momentakh evoliutcionnogo protcessa s tochki zreniia sovremennoi genetiki [On some moments of evolutional process from the viewpoint of the modern genetics]. Biull. Moskovskogo obshchestva ispytatelei prirody. Otdel biologicheskii [Bull. Moskow Society of nature investigators. Biology department]. 1965;70(4). (in Russian)

Soifer V. Ochen lichnaia kniga. Vospominaniia o velikikh rossiiskikh uchenykh Sergee Chetverikove i Nikolae Timofeeve-Resovskom [A very private book. Memoirs on the great Russian scientists S. Chetverikov and Nikolai Timofeev-Resovski.]. Novyi Mir. 2009;3. (in Russian). Available from: https://magazines.gorky.media/novyi_mi/2009/3/ochen-lichnaya-kniga.html

Danilov VI, Kventcel GF. Elektronnye predstavleniia v teorii tochechnykh mutatcii [Electronic representations in point mutation theory]. Kyiv: Naukova dumka; 1971. 84 p. (in Russian)

Meselson M, Stahl FW. The replication of DNA in Escherichia coli. PNAS. 1958;44(7):671–82. https://doi.org/10.1073/pnas.44.7.671

Friedberg EC, Walker GC, Siede W, Wood RD, Schultz RA, Ellenberger T. DNA repair and mutagenesis. 2nd ed. Washington: ASM Press; 2006. Part 3, DNA damage tolerance and mutagenesis. p. 461-750. https://doi.org/10.1128/9781555816704

Jonczyk P, Fijalkowska I, Ciesla Z. Overproduction of the subunit of DNA polymerase III counteracts the SOS mutagenic response of Escherichia coli. PNAS. 1988;85(23):9124–7. https://doi.org/10.1073/pnas.85.23.9124

Nee S. Deleterious mutation and genetic recombination. Nature. 1988;331:308. https://doi.org/10.1038/331308a0

Timoféeff-Ressovsky NW, Zimmer KG, Delbrück M. Über die Natur der Genmutation und der Genstruktur. Nachrichten der Gesellschaft der Wissenschaften zu Göttingen (VI). 1935;1:189–245. Available from: https://www.ini.uzh.ch/~tobi/fun/max/timofeeffZimmerDelbruck1935.pdf

Schrödinger E. What is life? The Physical Aspect of the Living Cell. Cambridge University Press; 1944. 194 p.

Fischer EP. Max Delbrück. Genetics. 2007;177(2):673–6. Available from: https://www.genetics.org/content/177/2/673.article-info

Bohr N. Light and Life. Nature. 1933;131:421–3. https://doi.org/10.1038/131421a0

Fischer EP, Lipson CP. Thinking About Science: Max Delbrück and the Origin of Molecular Biology. New York: W.W. Norton & Co Inc. 1988. 334 p. ISBN: 978-0393025088

Bohr N. Licht und Leben-noch einmal. Naturwissenschaften. 1963;50:725–7. https://doi.org/10.1007/BF00627713 (in German)

Topal MD, Fresco JR. Complementary base pairing and the origin of substitution mutations. Nature. 1976;263:285–9. https://doi.org/10.1038/263285a0

Goodman MF. Mutations caught in the act. Nature. 1995;378:237–8. https://doi.org/10.1038/378237a0

Brovarets' OO, Hovorun DM. Tautomeric transition between wobble A∙C DNA base mispair and Watson-Crick-like A∙C* mismatch: microstructural mechanism and biological significance. Phys Chem Chem Phys. 2015;17:15103–10. https://doi.org/10.1039/c5cp01568e

Freese EB. On the molecular explanation of spontaneous and induced mutations. Brookhaven Symp Biol. 1959;12:63–75.

Pullman B, Pullman A. Electronic aspects of purine tautomerism. Adv Heterocycl Chem. 1971;13:77–159. https://doi.org/10.1016/S0065-2725(08)60349-9

Kwiatkowski JS, Pullman B. Tautomerism and electronic structure of biological pyrimidines. Adv Heterocycl Chem. 1975;18:199–335. https://doi.org/10.1016/S0065-2725(08)60131-2

Colominas C, Luque FJ, Orozco M. Tautomerism and protonation of guanine and cytosine. Implications in the formation of hydrogen-bonded complexes. J Am Chem Soc. 1996;118(29):6811–21. https://doi.org/10.1021/ja954293l

Clementi E. Structure of water and counter ions for nucleic acids in solution. In: Clementi E, Sarma RH, editors. Structure and Dynamics: Nucleic Acids and Proteins. N.Y.: Academic Press; 1983. p. 321–64.

Masoodi HR, Bagheri S, Abareghi M. The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study. J Biomol Struct Dyn. 2016;34(6):1143–55. https://doi.org/10.1080/07391102.2015.1072734

Löwdin P-O. Proton tunneling in DNA and its biological implications. Rev Mod Phys. 1963;35:724. https://doi.org/10.1103/RevModPhys.35.724

Löwdin P-O. Effect of Proton Tunnelling in DNA on Genetic Information and Problems of Mutations, Aging, and Tumors. Biopolymers Symp. 1964;1:161–81.

Brovarets' ОО, Hovorun DN. How stable are the mutagenic tautomers of DNA bases? Biopolym Cell. 2010;26(1):72–6. https://doi.org/10.7124/bc.000147 (in Ukrainian).

Löwdin P-O. The mathematical definition of a molecule and molecular structure. In: Maruani J, editor. Molecules in physics, chemistry, and biology. Physical aspects of molecular systems. Volume 2. Dordrecht: Springer; 1988. p. 3–60. https://doi.org/10.1007/978-94-009-2851-0

Löwdin P-O. On nuclear motion and the definition of molecular structure. J Mol Struct: THEOCHEM. 1991;230:13–5. https://doi.org/10.1016/0166-1280(91)85169-8

McNaught AD, Wilkinson A. IUPAC Compendium of Chemical Terminology (the "Gold Book"). 2nd ed. Oxford: Blackwell Scientific Publications; 1997. Available from: http://goldbook.iupac.org

Brovarets' OO, Hovorun DM. Proton tunnelling in the AT Watson-Crick DNA base pair: myth or reality? J Biomol Struct Dyn. 2015;33:2716–20. https://doi.org/10.1080/07391102.2015.1092886

Godbeer AD, Al-Khalili JS, Stevenson PD. Modelling proton tunnelling in the adenine-thymine base pair. Phys Chem Chem Phys. 2015;17:13034–44. https://doi.org/10.1039/C5CP00472A

Florián J, Hrouda V, Hobza V. Proton transfer in the adenine-thymine base pair. J Am Chem Soc. 1994;116(4):1457–60. https://doi.org/10.1021/ja00083a034

Platt JR. Chemical aspects of genetics. Annu Rev Phys Chem. 1965;16:503–24. https://doi.org/10.1146/annurev.pc.16.100165.002443

Löwdin P-O. Some Properties of the Hydrogen Bonds in Biochemistry with Particular Reference to the Stability of the Genetic Code. Pontificiae Academiae Scientiarum. Scripta Varia. Semaine d'Etude sur les Forces Moléculaires, 18-23 avril 1966. 1967 ;31:637–708.

Frank-Kamenetskii MD. Fluktuatcionnaia podvizhnost DNK [Fluctuation mobility of DNA]. Mol Biol. (Moscow). 1983;17:639–52. (in Russian)

Frank-Kamenetskii MD, Prakash S. Fluctuations in the DNA double helix: A critical review. Phys Life Rev. 2014;11(2):153–70. https://doi.org/10.1016/j.plrev.2014.01.005

Jacobson B. Hydration structure of deoxyribonucleic acid and its physico-chemical properties. Nature. 1953;172:666–7. https://doi.org/10.1038/172666a0

Semenov MA, Maleev VYa. Energetika gidratatcii DNK [Energetics of DNA hydration]. Biophysics (Russian). 1986; 31(5):764–71. (in Russian)

Maleev VYa, Semenov MA, Gasan AI. Energeticheskie aspekty gidratatcii DNK [Energetic aspects of the hydration of DNA]. In: Ravnovesnaia dinamika struktury biopolimerov [Equilibrium dynamics of biopolymers' structure]. Pushhino; 1990. (in Russian)

Yanson IK, Teplitsky AB, Sukhodub LF. Experimental studies of molecular interactions between nitrogen bases of nucleic acids. Biopolymers. 1979;18(5):1149–70. https://doi.org/10.1002/bip.1979.360180510

Verkin BI, Yanson IK, Sukhodub LF. Vzaimodeistviia biomolekul: Novye eksperimentalnye podkhody i metody [The interactions of biomolecules: New experimental approaches and methods]. Kyiv: Naukova Dumka; 1985. 164 p. (in Russian)

Perepelytsya SM. Dynamical ordering of metal ions around DNA double helix. Visn Nac Akad Nauk Ukr. 2014;1:89–95. (In Ukrainian). https://doi.org/10.15407/visn2014.01.089

Eisenberg B. Computing the field in proteins and channels. J Membrane Biol. 1996;150:1–25. https://doi.org/10.1007/s002329900026

Goldblum A, Perahia D, Pullman A. Hydration scheme of the complementary base-pairs of DNA, FEBS Lett. 1978;91(2):213–5. https://doi.org/10.1016/0014-5793(78)81175-2

Clementi E, Corongiu G. A theoretical study of the water structure for nucleic acids bases and base pairs in solution at T=300K. J Chem Phys. 1980;72(7):3979–92. https://doi.org/10.1063/1.439676

Clementi E. Structure of water and counterions for nucleic acids in solution. In: Clementi E, Sarma RH, editors. Structure and Dynamics: Nucleic Acids and Proteins. New York: Adenine Press; 1983. p. 321–64.

Kabeláč M, Zendlova L, Řeha D, Hobza P. Potential energy surfaces of an adenine-thymine base pair and its methylated analogue in the presence of one and two water molecules: Molecular mechanics and correlated ab initio study. J Phys Chem B. 2005;109(24):12206–13. https://doi.org/10.1021/jp045970d

Poltev VI, Gonzalez EH, Teplukhin AV. Possible role of rare tautomers of DNA bases in mutagenesis: Evaluation of hydration effect on tautomeric equilibrium by Monte Carlo simulation. Mol Biol. (Moscow). 1995;29(2): 213–9.

Danilov VI, Dailidonis VV, Mourik T, Fruchtl HA. A study of nucleic acid base-stacking by the Monte Carlo method: Extended cluster approach. Cent Eur J Chem. 2011;9(4):720–7. https://doi.org/10.2478/s11532-011-0056-0

Kryachko ES, Volkov SN. Preopened states of DNA base pair. Physics of the Alive. 2000;7(2):118–24.

Kryachko ES, Volkov SN. Preopening of the DNA base pairs. Int J Quantum Chem. 2001;82:193–204. https://doi.org/10.1002/qua.1040

Giudice E, Várnai P, Lavery R. Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucl Acids Res. 2003;31(5):1434–43. https://doi.org/10.1093/nar/gkg239

van Aalten DMF, Erlanson DA, Verdine GL, Joshua-Tor L. A structural snapshot of base-pair opening in DNA. PNAS. 1999;96(21):11809–14. https://doi.org/10.1073/pnas.96.21.11809

Diekmann S. Definitions and nomenclature of nucleic acid structure parameters. J Mol Biol. 1989;205(4):787–91. https://doi.org/10.1016/0022-2836(89)90324-0

Jaroff I. The gene hunt. Time. 1989;133(12):62–7.

Published
2020-09-15
Cited
How to Cite
Kryachko, E. S. (2020). Hydrogen bonding and DNA: 66-year retrospective (briefly). Biophysical Bulletin, (43), 148-173. https://doi.org/10.26565/2075-3810-2019-43-15
Section
Discussions