Skip to main content
SpringerLink
Log in

Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides: Broad View and Novel Findings

  • Chapter
  • First Online:
Application of Computational Techniques in Pharmacy and Medicine

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 17))

  • 1625 Accesses

Abstract

In this chapter we analyze and systematize the data related to intramolecular hydrogen bonds and their impact on molecular geometry of nucleotides. The application of various non-empirical methods of quantum chemistry to determination of conformational characteristics of anions of the canonical 2′-deoxyribonucleotides and their methyl esters, as well as their energetics, is discussed. We revealed an existence of novel intramolecular interactions of the canonical 2′-deoxyribonucleotide anions. They are caused by incorporation of 2′-deoxyribonucleotide anions into DNA as well as by the impact of the nucleobases on the conformational features of the nucleotides and intramolecular interactions of these molecules. The efficient strategy of the evaluation of proton affinity for the different types of nucleotides is described. It is based on the analysis of consequences of nucleobases protonation along with the details of intramolecular interactions in 2′-deoxyribonucleotide anions. The results of our molecular simulations cast light on relationship between the conformational dynamics of a molecule and the tautomeric transitions in the components of nucleotides.

To the memory of Dr. Oleg Shishkin, our friend and colleague, for all inspiration he had continuously provided.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Saenger W (1988) Principles of nucleic acid structures. Springer, New York

    Google Scholar 

  2. Neidle S (1994) DNA Structure and recognition. Oxford University Press, Oxford

    Google Scholar 

  3. Sinden RSR (1994) DNA structure and function. Academic Press, San Diego

    Google Scholar 

  4. Hecht SM (1996) Bioorganic chemistry: nucleic acids. Oxford University Press, Oxford

    Google Scholar 

  5. Chu CK, Baker DC (1993) Nucleosides and nucleotides as antitumor and antiviral agents. Plenum Press, New York

    Book  Google Scholar 

  6. Sato T (1984) Structure of calcium thymidine 5′-phosphate dihydrate, Ca2+.C10H13N2O8P2–.2H2O. Acta Crystallogr Sect C Cryst Struct Commun 40:736–738. doi:10.1107/S0108270184005539

    Article  Google Scholar 

  7. Trueblood KN, Horn P, Luzzati V (1961) The crystal structure of calcium thymidylate. Acta Crystallogr 14:965–982. doi:10.1107/S0365110X61002801

    Article  CAS  Google Scholar 

  8. Lalitha HN, Ramakumar S, Viswamitra MA (1989) Structure of 5-methyl-2′-deoxycytidine 5′-monophosphate dihydrate. Acta Crystallogr Sect C Cryst Struct Commun 45:1652–1655. doi:10.1107/S0108270189005445

    Article  Google Scholar 

  9. Jardetsky O, Roberts GCK (1981) NMR in molecular biology. Academic Press, New York

    Google Scholar 

  10. Sundaralingam M (1973) Conformation of biological molecules and polymers. Jerus Symp Quant Chem Biochem 5:417.

    CAS  Google Scholar 

  11. Sundaralingam M (1975) Structure and conformation of nucleic acid and protein–nucleic acid interactions. University of Baltimore, Baltimore

    Google Scholar 

  12. Foloppe N, Hartmann B, Nilsson L, MacKerell AD (2002) Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophysical J 82:1554–1569. doi:10.1016/S0006-3495(02)75507-0

    Article  CAS  Google Scholar 

  13. Leulliot N, Ghomi M, Scalmani G, Berthier G (1999) Ground state properties of the nucleic acid constituents studied by density functional calculations. I. Conformational features of ribose, dimethyl phosphate, uridine, cytidine, 5′-methyl phosphate-uridine, and 3′-methyl phosphate-uridine. J Phys Chem A 103:8716–8724. doi: 10.1021/jp9915634

    Article  CAS  Google Scholar 

  14. Leulliot N, Ghomi M, Jobic H et al (1999) Ground state properties of the nucleic acid constituents studied by density functional calculations. 2. Comparison between calculated and experimental vibrational spectra of uridine and cytidine. J Phys Chem B 103:10934–10944. doi:10.1021/jp9921147

    Article  CAS  Google Scholar 

  15. Hocquet A, Leulliot N, Ghomi M (2000) Ground-state properties of nucleic acid constituents studied by density functional calculations. 3. Role of sugar puckering and base orientation on the energetics and geometry of 2′-deoxyribonucleosides and ribonucleosides. J Phys Chem B 104:4560–4568. doi:10.1021/jp994077p

    Article  CAS  Google Scholar 

  16. Foloppe N, MacKerell AD (1999) Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA. Biophysical J 76:3206–3218. doi:10.1016/S0006-3495(99)77472-2

    Article  CAS  Google Scholar 

  17. Gaigeot M-P, Leulliot N, Ghomi M et al (2000) Analysis of the structural and vibrational properties of RNA building blocks by means of neutron inelastic scattering and density functional theory calculations. Chem Phys 261:217–237. doi:10.1016/S0301-0104(00)00224-X

    Article  CAS  Google Scholar 

  18. Shishkin OV, Pelmenschikov A, Hovorun DM, Leszczynski J (2000) Molecular structure of free canonical 2′-deoxyribonucleosides: a density functional study. J Mol Struct 526:329–341. doi:10.1016/S0022-2860(00)00497-X

    Article  CAS  Google Scholar 

  19. Shishkin O V, Gorb L, Zhikol OA, Leszczynski J (2004) Conformational analysis of canonical 2-deoxyribonucleotides. 1. Pyrimidine nucleotides. J Biomol Struct Dyn 21:537–554. doi:10.1080/07391102.2004.10506947

    Article  CAS  Google Scholar 

  20. Shishkin OV, Gorb L, Zhikol OA, Leszczynski J (2004) Conformational analysis of canonical 2-deoxyribonucleotides. 2. Purine nucleotides. J Biomol Struct Dyn 22:227–244. doi:10.1080/07391102.2004.10506998

    Article  CAS  Google Scholar 

  21. Gorb L, Shishkin O, Leszczynski J (2005) Charges of phosphate groups. A role in stabilization of 2′-deoxyribonucleotides. A DFT investigation. J Biomol Struct Dyn 22:441–454. doi:10.1080/07391102.2005.10507015

    Article  CAS  Google Scholar 

  22. Šponer J, Leszczynski J, Hobza P (1996) Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with Inclusion of electron correlation. J Phys Chem 100:1965–1974. doi:10.1021/jp952760f

    Article  Google Scholar 

  23. Šponer J, Leszczyński J, Hobza P (1996) Nature of nucleic acid–base stacking: nonempirical ab initio and empirical potential Characterization of 10 stacked base dimers. comparison of stacked and h-bonded base pairs. J Phys Chem 100:5590–5596. doi:10.1021/jp953306e

    Article  Google Scholar 

  24. Šponer J, Burda J V., Sabat M et al (1998) Interaction between the guanine–cytosine Watson–Crick DNA base pair and hydrated group IIa (Mg 2+, Ca 2+, Sr 2+, Ba 2+ ) and group IIb (Zn 2+, Cd 2+, Hg 2+ ) metal cations. J Phys Chem A 102:5951–5957. doi:10.1021/jp980769m

    Google Scholar 

  25. Řeha D, KabelácÌ M, RyjácÌek F et al (2002) Intercalators. 1. nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4′,6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, Density functional theory, and empirical potential study. J American Chem Soc 124:3366–3376. doi:10.1021/ja011490d

    Article  Google Scholar 

  26. Spacková N, Cheatham TE, Ryjácek F et al (2003) Molecular dynamics simulations and thermodynamics analysis of DNA–drug complexes. Minor groove binding between 4′,6-diamidino-2-phenylindole and DNA duplexes in solution. J Am Chem Soc 125:1759–1769. doi:10.1021/ja025660d

    Article  Google Scholar 

  27. Shishkin O V, Gorb L, Luzanov A V et al (2003) Structure and conformational flexibility of uracil:a comprehensive study of performance of the MP2, B3LYP and SCC-DFTB methods. J Mol Struct: Theochem 625:295–303. doi:10.1016/S0166-1280(03)00032-0

    Article  CAS  Google Scholar 

  28. Gorb L, Kaczmarek A, Gorb A et al (2005) Thermodynamics and kinetics of intramolecular proton transfer in guanine. Post Hartree-Fock study. J Phys Chem B 109:13770–13776. doi:10.1021/jp050394m

    Article  CAS  Google Scholar 

  29. Isayev O, Furmanchuk A, Shishkin O V et al (2007) Are isolated nucleic acid bases really planar? A Car-Parrinello molecular dynamics study. J phys chem B 111:3476–3480. doi:10.1021/jp070857j

    Article  CAS  Google Scholar 

  30. Samijlenko SP, Yurenko YP, Stepanyugin A V, Hovorun DM (2010) Tautomeric equilibrium of uracil and thymine in model protein–nucleic acid contacts. Spectroscopic and quantum chemical approach. J phys chem B 114:1454–1461. doi:10.1021/jp909099a

    Article  CAS  Google Scholar 

  31. Shishkin O V, Palamarchuk G V, Gorb L, Leszczynski J (2006) Intramolecular hydrogen bonds in canonical 2′-deoxyribonucleotides: an atoms in molecules study. J phys chem B 110:4413–4422. doi:10.1021/jp056902+

    Article  CAS  Google Scholar 

  32. Slavícek P, Winter B, Faubel M et al (2009) Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations. J Am Chem Soc 131:6460–6467. doi:10.1021/ja8091246

    Article  Google Scholar 

  33. Sapse DS, Champeil É, Maddaluno J et al (2008) An ab initio study of the interaction of DNA fragments with methyllithium. C R Chim 11:1262–1270. doi:10.1016/j.crci.2008.04.009

    Article  CAS  Google Scholar 

  34. Yurenko YP, Zhurakivsky RO, Ghomi M et al (2007) How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study. J Phys Chem B 111:9655–9663. doi:10.1021/jp073203j

    Article  CAS  Google Scholar 

  35. Yurenko YP, Zhurakivsky RO, Ghomi M et al (2007) Comprehensive conformational analysis of the nucleoside analogue 2′-beta-deoxy-6-azacytidine by DFT and MP2 calculations. J Phys Chem B 111:6263–6271. doi:10.1021/jp066742h

    Article  CAS  Google Scholar 

  36. Shishkin OV, Pelmenschikov A, Hovorun DM, Leszczynski J (2000) Molecular structure of free canonical 2′-deoxyribonucleosides: a density functional study. J Mol Struct 526:329–341. doi:10.1016/S0022-2860(00)00497-X

    Article  CAS  Google Scholar 

  37. Hobza P, Šponer J (1999) Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem Rev 99:3247–3276. doi:10.1021/cr9800255

    Article  CAS  Google Scholar 

  38. Sponer J, Leszczynski J, Hobza P (2002) Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers 61:3–31. doi:10.1002/1097-0282 (2001) 61:1 < 3::AID-BIP10048>3.0.CO;2–4

    Google Scholar 

  39. Svozil D, Kalina J, Omelka M, Schneider B (2008) DNA conformations and their sequence preferences. Nucleic acids res 36:3690–3706. doi:10.1093/nar/gkn260

    Article  CAS  Google Scholar 

  40. Schneider B, Neidle S, Berman HM (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42:113–124. doi:10.1002/(SICI)1097-0282(199707)42:1 < 113::AID-BIP10 > 3.0.CO;2–O

    Google Scholar 

  41. Drew HR, Wing RM, Takano T et al (1981) Structure of a B-DNA dodecamer: conformation and dynamics. PNAS 78:2179.

    Article  CAS  Google Scholar 

  42. Grzeskowiak K, Yanagi K, Privé GG, Dickerson and RE (1991) The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals. J Biol Chem 266:8861.

    CAS  Google Scholar 

  43. Shishkin OV, Gorb L, Luzanov AV et al (2003) Structure and conformational flexibility of uracil: a comprehensive study of performance of the MP2, B3LYP and SCC-DFTB methods. J Mol Struct: Theochem 625:295–303. doi:10.1016/S0166-1280(03)00032-0

    Article  CAS  Google Scholar 

  44. Bader RFW (1990) Atoms in molecules. A quantum theory. Clarendon, Oxford

    Google Scholar 

  45. Popelier PLA (1998) Characterization of a dihydrogen bond on the basis of the electron density. J Phys Chem A 102:1873–1878. doi: 10.1021/jp9805048

    Article  CAS  Google Scholar 

  46. Koch U, Popelier PLA (1995) Characterization of C–H–O hydrogen bonds on the basis of the charge density. J Phys Chem 99:9747–9754. doi:10.1021/j100024a016

    Article  CAS  Google Scholar 

  47. Cremer D, Kraka E, Slee TS et al (1983) Description of homoaromaticity in terms of electron distributions. J Am Chem Soc 105:5069–5075. doi:10.1021/ja00353a036

    Article  CAS  Google Scholar 

  48. Hocquet A (2001) Intramolecular hydrogen bonding in 2′-deoxyribonucleosides: an AIM topological study of the electronic density. Phys Chem Chem Phys 3:3192–3199. doi:10.1039/b101781k

    Article  CAS  Google Scholar 

  49. Zefirov YV., Zorky PM (1989) No title. Uspekhi Khimii (Russian Chemical Rev) 58:713.

    CAS  Google Scholar 

  50. Thomas Steiner (2002) The hydrogen bond in the solid state. Angew Chem Int Ed 41:48. doi:10.1002/1521-3773(20020104)41:1<48::AID-ANIE48>3.0.CO;2–U

    Google Scholar 

  51. Hocquet A, Ghomi M (2000) The peculiar role of cytosine in nucleoside conformational behaviour: hydrogen bond donor capacity of nucleic bases. Phys Chem Chem Phys 2:5351–5353. doi:10.1039/b007246j

    Article  CAS  Google Scholar 

  52. Shishkin OV, Palamarchuk GV, Gorb L, Leszczynski J (2006) Intramolecular hydrogen bonds in canonical 2′-deoxyribonucleotides: an atoms in molecules study. J Phys Chem B 110:4413–4422. doi:10.1021/jp056902+

    Article  CAS  Google Scholar 

  53. Palamarchuk GV, Shishkin OV, Gorb L, Leszczynski J (2009) Dependence of deformability of geometries and characteristics of intramolecular hydrogen bonds in canonical 2′-deoxyribonucleotides on DNA conformations. J Biomol Struct Dyn 26:653–662. doi:10.1080/07391102.2009.10507279

    Article  CAS  Google Scholar 

  54. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789. doi:10.1103/PhysRevB.37.785

    Article  CAS  Google Scholar 

  55. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098–3100. doi: 10.1103/PhysRevA.38.3098

    Article  CAS  Google Scholar 

  56. Parr RG, Yang W (1989) Density functional theory of atoms and molecules. Oxford University Press, New York

    Google Scholar 

  57. Cammi R, Mennucci B, Tomasi J (2000) Fast evaluation of geometries and properties of excited molecules in solution: a Tamm-Dancoff model with application to 4-dimethylaminobenzonitrile. J Phys Chem A 104:5631–5637. doi:10.1021/jp000156l

    Article  CAS  Google Scholar 

  58. Cossi M, Scalmani G, Rega N, Barone V (2002) New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution. J Chem Phys 117:43. doi: 10.1063/1.1480445

    Article  CAS  Google Scholar 

  59. Miertuš S, Scrocco E, Tomasi J (1981) Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects. Chem Phys 55:117–129. doi:10.1016/0301-0104(81)85090-2

    Article  Google Scholar 

  60. Lee H-T, Khutsishvili I, Marky LA (2010) DNA complexes containing joined triplex and duplex motifs: melting behavior of intramolecular and bimolecular complexes with similar sequences. J Phys Chem B 114:541–548. doi:10.1021/jp9084074

    Article  CAS  Google Scholar 

  61. Frank-Kamenetskii MD, Mirkin SM (1995) Triplex DNA structures. Annu Rev Biochem 64:65–95. doi:10.1146/annurev.bi.64.070195.000433

    Article  CAS  Google Scholar 

  62. Jissy AK, Datta A (2010) Designing molecular switches based on DNA–base mispairing. J Phys Chem B 114:15311–15318. doi:10.1021/jp106732u

    Article  CAS  Google Scholar 

  63. Hunter WN, Brown T, Anand NN, Kennard O Structure of an adenine–cytosine base pair in DNA and its implications for mismatch repair. Nature 320:552–555. doi:10.1038/320552a0

    Google Scholar 

  64. Lowdin PO (1965) Quantum genetics and the aperiodic solid: some aspects on the biological problems of heredity, mutations, aging, and tumors in view of the quantum theory of the dna molecule. Adv Quant Chem 2:213–354. doi:10.1016/S0065-3276(08)60076-3

    Article  CAS  Google Scholar 

  65. Florián J, Leszczyński J (1996) Spontaneous DNA mutations induced by proton transfer in the guanine·cytosine base pairs: an energetic perspective. J Am Chem Soc 118:3010–3017. doi:10.1021/ja951983g

    Article  Google Scholar 

  66. Šponer J, Šponer JE, Gorb L et al (1999) Metal-stabilized rare tautomers and mispairs of DNA bases: N6-metalated adenine and N4-metalated cytosine, theoretical and experimental views. J Phys Chem A 103:11406–11413. doi:10.1021/jp992337x

    Article  Google Scholar 

  67. O’Brien PJ, Ellenberger T (2003) Human alkyladenine DNA glycosylase uses acid-base catalysis for selective excision of damaged purines. Biochemistry 42:12418–12429. doi:10.1021/bi035177v

    Article  Google Scholar 

  68. Rios-Font R, Rodríguez-Santiago L, Bertran J, Sodupe M (2007) Influence of N7 protonation on the mechanism of the N-glycosidic bond hydrolysis in 2′-deoxyguanosine. A theoretical study. J phys chem B 111:6071–6077. doi: 10.1021/jp070822j

    Article  CAS  Google Scholar 

  69. Chen X-Y, Berti PJ, Schramm VL (2000) Ricin a-chain: kinetic isotope effects and transition state structure with stem-loop RNA †. J Am Chem Soc 122:1609–1617. doi:10.1021/ja992750i

    Article  CAS  Google Scholar 

  70. Francis AW, Helquist SA, Kool ET, David SS (2003) Probing the requirements for recognition and catalysis in Fpg and MutY with nonpolar adenine isosteres. J Am Chem Soc 125:16235–16242. doi:10.1021/ja0374426

    Article  CAS  Google Scholar 

  71. Kennedy SA, Novak M, Kolb BA (1997) Reactions of ester derivatives of carcinogenic N-(4-Biphenylyl)hydroxylamine and the corresponding hydroxamic acid with purine nucleosides. J Am Chem Soc 119:7654–7664. doi:10.1021/ja970698p

    Article  CAS  Google Scholar 

  72. McClelland RA, Ahmad A, Dicks AP, Licence VE (1999) Spectroscopic characterization of the initial c8 intermediate in the reaction of the 2-fluorenylnitrenium Ion with 2′deoxyguanosine. J Am Chem Soc 121:3303–3310. doi:10.1021/ja9836702

    Article  CAS  Google Scholar 

  73. Qi S-F, Wang X-N, Yang Z-Z, Xu X-H (2009) Effect of N7-protonated purine nucleosides on formation of C8 adducts in carcinogenic reactions of arylnitrenium ions with purine nucleosides: a quantum chemistry study. J Phys Chem B 113:5645–5652. doi:10.1021/jp811262x

    Article  CAS  Google Scholar 

  74. Shishkin OV, Dopieralski P, Palamarchuk GV, Latajka Z (2010) Rotation around the glycosidic bond as driving force of proton transfer in protonated 2′-deoxyriboadenosine monophosphate (dAMP). Chem Phys Lett 490:221–225. doi:10.1016/j.cplett.2010.03.044

    Article  CAS  Google Scholar 

  75. Green-Church KB, Limbach PA (2000) Mononucleotide gas-phase proton affinities as determined by the kinetic method. J Am Soc Mass Spectrom 11:24–32. doi:10.1016/S1044-0305(99)00116-6

    Article  CAS  Google Scholar 

  76. Green-Church KB, Limbach PA, Freitas MA, Marshall AG (2001) Gas-phase hydrogen/deuterium exchange of positively charged mononucleotides by use of Fourier-transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 12:268–277. doi:10.1016/S1044-0305(00)00222-1

    Article  CAS  Google Scholar 

  77. Pan S, Verhoeven K, Lee JK (2005) Investigation of the initial fragmentation of oligodeoxynucleotides in a quadrupole ion trap: charge level-related base loss. J Am Soc Mass Spectrom 16:1853–1865. doi:10.1016/j.jasms.2005.07.009

    Article  CAS  Google Scholar 

  78. Shishkin OV, Palamarchuk GV, Gorb L, Leszczynski J (2008) Opposite charges assisted extra strong C–H…O hydrogen bond in protonated 2′-deoxyadenosine monophosphate. Chem Phys Lett 452:198–205. doi:10.1016/j.cplett.2007.12.052

    Article  CAS  Google Scholar 

  79. Ebrahimi A, Habibi-Khorassani M, Bazzi S (2011) The impact of protonation and deprotonation of 3-methyl-2′-deoxyadenosine on N-glycosidic bond cleavage. Phys Chem Chem Phys: PCCP 13:3334–3343. doi:10.1039/c0cp01279c

    Article  CAS  Google Scholar 

  80. Berti PJ, Tanaka KSE (2002) No title. Adv Phys Org Chem 37:239–314.

    CAS  Google Scholar 

  81. Loverix S, Geerlings P, McNaughton M et al (2005) Substrate-assisted leaving group activation in enzyme-catalyzed N-glycosidic bond cleavage. J Biol Chem 280:14799–14802. doi:10.1074/jbc.M413231200

    Article  CAS  Google Scholar 

  82. Mol CD, Parikh SS, Putnam CD et al (1999) DNA repair mechanisms for the recognition and removal of damaged DNA bases. Annu Rev Biophys and Biomol Struct 28:101–128. doi:10.1146/annurev.biophys.28.1.101

    Article  CAS  Google Scholar 

  83. Cao C, Kwon K, Jiang YL et al (2003) Solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I. J Biol Chem 278:48012–48020. doi: 10.1074/jbc.M307500200

    Article  CAS  Google Scholar 

  84. Palamarchuk GV, Shishkin OV, Gorb L, Leszczynski J (2013) Nucleic acid bases in anionic 2′-deoxyribonucleotides: a DFT/B3LYP study of structures, relative stability, and proton affinities. J Phys Chem B 117:2841–2849. doi:10.1021/jp311363c

    Article  CAS  Google Scholar 

  85. Gonnella NC, Nakanishi H, Holtwick JB et al (1983) Studies of tautomers and protonation of adenine and its derivatives by nitrogen-15 nuclear magnetic resonance spectroscopy. J Am Chem Soc 105:2050–2055. doi:10.1021/ja00345a063

    Article  CAS  Google Scholar 

  86. Brown RD, Godfrey PD, McNaughton D, Pierlot AP (1989) A study of the major gas-phase tautomer of adenine by microwave spectroscopy. Chem Phys Lett 156:61–63. doi:10.1016/0009-2614(89)87081-2

    Article  CAS  Google Scholar 

  87. Lias SG, Liebman JF, Levin RD (1984) Evaluated gas phase basicities and proton affinities of molecules; heats of formation of protonated molecules. J Phys Chem Ref Data 13:695. doi:10.1063/1.555719

    Article  CAS  Google Scholar 

  88. Greco F, Liguori A, Sindona G, Uccella N (1990) Gas-phase proton affinity of deoxyribonucleosides and related nucleobases by fast atom bombardment tandem mass spectrometry. J the American Chem Soc 112:9092–9096. doi:10.1021/ja00181a009

    Article  CAS  Google Scholar 

  89. Meot-Ner M (1979) Ion thermochemistry of low-volatility compounds in the gas phase. 2. Intrinsic basicities and hydrogen-bonded dimers of nitrogen heterocyclics and nucleic bases. J Am Chem Soc 101:2396–2403. doi:10.1021/ja00503a027

    Article  CAS  Google Scholar 

  90. Kurinovich MA, Lee JK (2000) The acidity of uracil from the gas phase to solution: the coalescence of the N1 and N3 sites and implications for biological glycosylation. J Am Chem Soc 122:6258–6262. doi:10.1021/ja000549y

    Article  CAS  Google Scholar 

  91. Kurinovich MA, Lee JK (2002) The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications. J Am Soc Mass Spectrom 13:985–995. doi:10.1016/S1044-0305(02)00410-5

    Article  CAS  Google Scholar 

  92. Liu M, Li T, Amegayibor FS et al (2008) Gas-phase thermochemical properties of pyrimidine nucleobases. J Org Chem 73:9283–9291. doi:10.1021/jo801822s

    Article  CAS  Google Scholar 

  93. Bonaccorsi R, Pullman A, Scrocco E, Tomasi J (1972) The molecular electrostatic potentials for the nucleic acid bases: adenine, thymine, and cytosine. Theor Chim Acta 24:51–60. doi:10.1007/BF00528310

    Article  CAS  Google Scholar 

  94. Russo N, Toscano M, Grand A, Jolibois F (1998) Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: theoretical investigation into the framework of density functional theory. J Comput Chem 19:989–1000. doi:10.1002/(SICI)1096-987X(19980715)19:9<989::AID-JCC1>3.0.CO;2–F

    Google Scholar 

  95. Colominas C, Luque FJ, Orozco M (1996) Tautomerism and protonation of guanine and cytosine. implications in the formation of hydrogen-bonded complexes. J Am Chem Soc 118:6811–6821. doi:10.1021/ja954293l

    Article  CAS  Google Scholar 

  96. Podolyan Y, Gorb L, Leszczynski J (2000) Protonation of nucleic acid bases. A comprehensive post-Hartree–Fock study of the energetics and proton affinities. J Phys Chem A 104:7346–7352. doi:10.1021/jp000740u

    Article  CAS  Google Scholar 

  97. Liguori A, Napoli A, Sindona G (2000) Survey of the proton affinities of adenine, cytosine, thymine and uracil dideoxyribonucleosides, deoxyribonucleosides and ribonucleosides. J Mass Spectrom: JMS 35:139–144. doi:10.1002/(SICI)1096-9888(200002)35:2<139::AID-JMS921>3.0.CO;2–A

    Article  CAS  Google Scholar 

  98. Di Donna L, Napoli A, Sindona G, Athanassopoulos C (2004) A comprehensive evaluation of the kinetic method applied in the determination of the proton affinity of the nucleic acid molecules. J Am Soc Mass Spectrom 15:1080–1086. doi:10.1016/j.jasms.2004.04.027

    Article  CAS  Google Scholar 

  99. Wilson MS, McCloskey JA (1975) Chemical ionization mass spectrometry of nucleosides. Mechanisms of ion formation and estimations of proton affinity. J Am Chem Soc 97:3436–3444. doi:10.1021/ja00845a026

    Article  CAS  Google Scholar 

  100. Gorb L, Podolyan Y, Dziekonski P et al (2004) Double-proton transfer in adenine-thymine and guanine–cytosine base pairs. A post-Hartree-Fock ab initio study. J Am Chem Soc 126:10119–10129. doi:10.1021/ja049155n

    Article  CAS  Google Scholar 

  101. Lukin M, De Los Santos C (2006) NMR structures of damaged DNA. Chem Rev 106:607–686. doi:10.1021/cr0404646

    Article  CAS  Google Scholar 

  102. Boussicault F, Robert M (2008) Electron transfer in DNA and in DNA-related biological processes. Electrochem insights. Chem Rev 108:2622–2645. doi:10.1021/cr0680787

    Article  CAS  Google Scholar 

  103. Giovangelle C, Sun JS, Helene C (1996) In comprehensive supramolecular chemistry. Pergamon Press, Oxford, p 177

    Google Scholar 

Download references

Acknowledgments

The authors thank the National Science Foundation for financial support through NSF/CREST Award (HRD-0833178). This research was supported in part by the Extreme Science and Engineering Discovery Environment (XSEDE) by National Science Foundation grant number OCI-1053575 and XSEDE award allocation number DMR110088. Authors thank to the Mississippi Center for Supercomputer Research (Oxford, MS) for the generous allotment of computer time. The support from computational facilities of joint computational cluster of SSI “Institute for Single Crystals” and Institute for Scintillation Materials of National Academy of Science of Ukraine incorporated into Ukrainian National Grid is gratefully acknowledged.

Author information

Authors and Affiliations

  1. SSI “Institute for Single Crystals” of National Academy of Science of Ukraine, Lenina Ave., 60, 61001, Kharkiv, Ukraine

    Tetiana A. Zubatiuk, Gennady V. Palamarchuk & Oleg V. Shishkin

  2. Laboratory of Computational Structural Biology, Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Key State Laboratory in Molecular and Cell Biology, 03143, Kyiv, Zabolotnogo Str., 150, Ukraine

    Leonid Gorb

  3. Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Lynch Str., 1325, P.O. Box 17910, 39217, Jackson, MS, USA

    Jerzy Leszczynski

Authors
  1. Tetiana A. Zubatiuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gennady V. Palamarchuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Oleg V. Shishkin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Leonid Gorb
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jerzy Leszczynski
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tetiana A. Zubatiuk .

Editor information

Editors and Affiliations

  1. Department of Molecular Biophysics, Laboratory of Computational Structural Biology, Kiev, Ukraine

    Leonid Gorb

  2. Department of Molecular Structure and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute, National Academy of Sciences of Ukraine, Odessa, Ukraine

    Victor Kuz'min

  3. Department of Chemical Biology and Medicinal Chemistry, University of North Carolina, Laboratory for Molecular Modeling, Chapel Hill, North Carolina, USA

    Eugene Muratov

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Zubatiuk, T., Palamarchuk, G., Shishkin, O., Gorb, L., Leszczynski, J. (2014). Molecular Structures, Relative Stability, and Proton Affinities of Nucleotides: Broad View and Novel Findings. In: Gorb, L., Kuz'min, V., Muratov, E. (eds) Application of Computational Techniques in Pharmacy and Medicine. Challenges and Advances in Computational Chemistry and Physics, vol 17. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9257-8_5

Download citation

Publish with us

Policies and ethics

Search

Navigation