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T. A. Zubatiuk et al.
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
61. Frank-Kamenetskii MD, Mirkin SM (1995) Triplex DNA structures. Annu Rev Biochem
64:65–95. doi:10.1146/annurev.bi.64.070195.000433
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
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
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
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
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
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
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
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
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
71. Kennedy SA, Novak M, Kolb BA (1997) Reactions of ester derivatives of carcinogenic N-(4Biphenylyl)hydroxylamine and the corresponding hydroxamic acid with purine nucleosides.
J Am Chem Soc 119:7654–7664. doi:10.1021/ja970698p
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
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
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
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/S10440305(99)00116-6
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
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
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
T. A. Zubatiuk et al.
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
61. Frank-Kamenetskii MD, Mirkin SM (1995) Triplex DNA structures. Annu Rev Biochem
64:65–95. doi:10.1146/annurev.bi.64.070195.000433
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
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
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
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
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
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
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
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
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
71. Kennedy SA, Novak M, Kolb BA (1997) Reactions of ester derivatives of carcinogenic N-(4Biphenylyl)hydroxylamine and the corresponding hydroxamic acid with purine nucleosides.
J Am Chem Soc 119:7654–7664. doi:10.1021/ja970698p
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
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
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
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/S10440305(99)00116-6
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
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
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