Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: Ab initio quantum-chemical and empirical potential study

被引:78
作者
Sponer, J
Burda, JV
Mejzlik, P
Leszczynski, J
Hobza, P
机构
[1] ACAD SCI CZECH REPUBL, INST BIOPHYS, CS-61265 BRNO, CZECH REPUBLIC
[2] MASARYK UNIV, FAC INFORMAT, BRNO 60200, CZECH REPUBLIC
[3] JACKSON STATE UNIV, DEPT CHEM, JACKSON, MS 39217 USA
关键词
D O I
10.1080/07391102.1997.10508161
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Neutral (G.GC, A.AT, G.AT, T.AT, and C(imino).GC) and protonated (CH+.GC and AH(+).GC) hydrogen-bonded trimers of nucleic acid bases were characterized by ab initio methods with the inclusion of electron correlation. In addition, the influence of metal cations on the third-strand binding in Purine-Purine-Pyrimidine (Pu.PuPy) reverse-Hoogsteen triplets has been studied. The ab initio calculations were compared with those from recently introduced force fields (AMBER4.1, CHARMM23, and CFF95). The three-body term in neutral trimers is mostly negligible, and the use of empirical potentials is justified. The only exception is the neutral G.GC Hoogsteen trimer with a three-body term of -4 kcal/mol. Protonated trimers are stabilized by molecular ion - molecular dipole attraction and the interaction within the complex is nonadditive, with the three-body term on the order of -3 kcal/mol. There is a significant induction interaction between the third-strand protonated base and guanine. The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to metal cation coordination to the N7/O6 position of the third-strand guanine. Interactions between metal cations and complexes of DNA bases are in general highly nonadditive; the three-body term is above -10 kcal/mol in a complex of a divalent cation (Ca2+) with the GG reverse-Hoogsteen pair. The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base.
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页码:613 / 628
页数:16
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共 102 条
[2]  
Alkorta I, 1996, INT J QUANTUM CHEM, V57, P123, DOI 10.1002/(SICI)1097-461X(1996)57:1<123::AID-QUA14>3.0.CO
[3]  
2-9
[4]   THE INFLUENCE OF LI+, NA+, MG-2+, CA-2+, AND ZN-2+ IONS ON THE HYDROGEN-BONDS OF THE WATSON-CRICK BASE-PAIRS [J].
ANWANDER, EHS ;
PROBST, MM ;
RODE, BM .
BIOPOLYMERS, 1990, 29 (4-5) :757-769
[5]   AN ANISOTROPIC POLARIZABLE WATER MODEL - INCORPORATION OF ALL-ATOM POLARIZABILITIES INTO MOLECULAR MECHANICS FORCE-FIELDS [J].
BERNARDO, DN ;
DING, YB ;
KROGHJESPERSEN, K ;
LEVY, RM .
JOURNAL OF PHYSICAL CHEMISTRY, 1994, 98 (15) :4180-4187
[6]  
BETTS L, 1996, SCIENCE, V270, P1038
[7]   CALCULATION OF SMALL MOLECULAR INTERACTIONS BY DIFFERENCES OF SEPARATE TOTAL ENERGIES - SOME PROCEDURES WITH REDUCED ERRORS [J].
BOYS, SF ;
BERNARDI, F .
MOLECULAR PHYSICS, 1970, 19 (04) :553-&
[8]   POLYNUCLEOTIDES .16. FORMATION OF THE TRIPLE-STRANDED POLYNUCLEOTIDE HELIX, POLY(A-A-U) [J].
BROITMAN, SL ;
IM, DD ;
FRESCO, JR .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1987, 84 (15) :5120-5124
[9]   Ab Initio study of the interaction of guanine and adenine with various mono- and bivalent metal cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+) [J].
Burda, JV ;
Sponer, J ;
Hobza, P .
JOURNAL OF PHYSICAL CHEMISTRY, 1996, 100 (17) :7250-7255
[10]  
BURDA JV, UNPUB J PHYS CHEM