Theoretical Studies on the Effect of Fapy-G on Base Pair Hydrogen Bond Complexes†

doi:10.7503/cjcu20140510

Abstract

Abstract:

One of the primary oxidative DNA damage is 2,6-diamino-4-hydroxy-5-formamido pyrimidine, named Fapy-guanine(Fapy-G), which is the product of guanine oxidized at C8. The properties of 20 oxidative base pairs which contains Fapy-G were investigated via quantum chemistry methods. All model molecular structures were optimized with B3LYP/6-31+G^* method and the frequency calculations were carried out to confirm that all the structures obtains were geometrically stable. The energies were determined at the MP2/aug-cc-pVDZ level with BSSE corrections. The calculation results show that N7, N9 became hydrogen bond donor from accepter. Natural atomic charge of N7, N9 and O6 get more negative. The ability of O6 as H-bond donor enhanced. The bond lengths of C5—N7 and N7—C8 were increased by 0.0045 and 0.0063 nm, C4—N9 was decreased by 0.0015 nm. Compared with bases monomers, natural atomic charge of proton acceptors in hydrogen bond complexes increased by 0.05 e averagely, which is 8% of the original charge; natural atomic charges for proton donors have a decrease of 0.02 e, which is 4% of the original charge. Compared with Fapy-G, when the N atom in Fapy-G six-membered ring was formed H-bond, the ring breathing and N-para-C vibrational frequencies were blue shifts. The vibrational frequencies were related to H-bond red shifts in all the base pairs. NH…N is stronger than NH…O in all the base pairs and in NH…N the hydrogen bond energy of donor N atom in six-membered ring are bigger than donor N atom in NH₂ or open-ring. When Fapy-G pairs with base A, the binding energy region order is 1>2>4>3. When Fapy-G pairs with base T(R), the binding energy region order is 3=4>1>2. In water solvent, the binding energies of Fapy-G pairs with base C reduced to 41.84—58.58 kJ/mol, and the order of the binding energy was changed.

Key words: Quantum chemical method, Oxidized base pair, Hydrogen bond, Charge population, Binding energy

CLC Number:

O641

TrendMD:

LIU Cui, ZHANG Qianhui, GONG Lidong, LU Linan, YANG Zhongzhi. Theoretical Studies on the Effect of Fapy-G on Base Pair Hydrogen Bond Complexes^†[J]. Chem. J. Chinese Universities, 2014, 35(12): 2645.

Figures/Tables 6

Fig.1 Geometry of G and the syn and anti geometries of Fapy-G The numbers without parentheses are the bond length(nm) in Fapy-G monomer. The numbers in parentheses denote the bond length(nm) in G monomer. The numbers 1—5 denote these regions, at which Fapy-G pairs with A, T, G, or C.

Fig.2 Oxidized base pairs containing Fapy-G WC represents Watson-Crick hydrogen bonding pattern. H represents Hoogsteen hydrogen bonding pattern. R represents reverse Watson-Crick or reverse Hoogsteen hydrogen bonding pattern.The hydrogen bond length are in nm. The number in bracket is the deviation angle.

Fig.3 Deviation angle of base pair plane

Table 1 Frequencies of the four kinds of infrared vibrational modes in monomer Fapy-G and the base pairs formed hydrogen bond at 3,4 regions

Molecule	ν₁/cm^-1	ν_6a/cm^-1	ν_8a/cm^-1	ν₁₂/cm^-1
Fapy-G	1058.65	610.98	1640.02	1293.97
Fapy-G3:A(H)	1060.63	612.45	1641.10	1299.20
Fapy-G3:A(WC)	1061.16	612.44	1641.30	1300.55
Fapy-G4:A(H)	1064.21	612.71	1633.37	1288.29
Fapy-G4:A(WC)	1064.98	614.25	1634.57	1289.78
Fapy-G4:C(WC)	1066.50	614.12	1636.79	1289.73
Fapy-G34:T1	1071.58	615.72	1636.70	1303.04
Fapy-G34:T2	1071.49	615.50	1637.90	1303.91

Fig.4 Natural atomic charges(e) formed hydrogen bond in G:C(A) and Fapy-G15:C(WC)(B) base pairs The numbers in parentheses mean natural atomic charges(e) in G, Fapy-G or C monomer. The numbers without parentheses mean natural atomic charges(e) of base pairs.

Fig.5 Order of binding energy(ΔEb)(A) and second-order stabilization energies (Esum)(B) of base pairs a. Region 1; b. region 2; c. region 3; d. region 4.

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