Non-canonical DNA structures: Comparative quantum mechanical study

被引：6

作者：

Bachurin, Stanislav S. ^{[1
]}

Kletskii, Mikhail E. ^{[2
]}

Burov, Oleg N. ^{[2
]}

Kuibatov, Sergey V. ^{[2
]}

机构：

[1] FSBEI HE Rostov State Med Univ, Minist Hlth Russian Federat, 29 Nakhichevansky St, Rostov Na Donu 344022, Russia

[2] Southern Fed Univ, Chem Fac, 7 Zorge St, Rostov Na Donu 344090, Russia

来源：

BIOPHYSICAL CHEMISTRY | 2018年 / 235卷

关键词：

Non-canonical DNA structure; G-quadruplex; Triplex; i-Motif; DFT calculations; I-MOTIF DNA; TRIPLE-HELIX FORMATION; G-QUADRUPLEX DNA; NUCLEIC-ACIDS; CROSS-LINKING; BASE-PAIRS; STABILITY; MOLECULES; PROMOTER; CYTOSINE;

D O I：

10.1016/j.bpc.2018.02.003

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：

A study of relative thermodynamic stability of non-canonical DNA structures (triplexes, G-quadruplexes, i-motifs) for the first time was conducted on the basis of quantum chemical DFT/B3LYP/6-31 + +G (d) calculations. Results of the calculations completely reproduce the experimental data on stability of G-quadruplexes comparatively Watson-Crick B-DNA. It was discovered that combinations of non-canonical DNA structures were energetically more favorable than separated nitrogenous bases. Supramolecular complexes of the non-canonical DNA structures (NSs) can be considered as a biological drug targets in gene regulation (for example in tumor therapy), in contrast to previous works, where NSs were studied independently.

引用

页码：19 / 28

页数：10

共 62 条

[1]

[Anonymous], HYPERCHEM TM PROF 7

[2] Oligonucleotide cross-linking with copper ions. Spectral and quantum chemical study [J].

Bachurin, S. S. ;

Faleeva, T. G. ;

Kletskii, M. E. ;

Burov, O. N. ;

Askalepova, O. I. ;

Kornienko, I. V. .

RUSSIAN JOURNAL OF GENERAL CHEMISTRY, 2016, 86 (12) :2647-2652

[3] Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? [J].

Balasubramanian, Shankar ;

Hurley, Laurence H. ;

Neidle, Stephen .

NATURE REVIEWS DRUG DISCOVERY, 2011, 10 (04) :261-275

[4] 2ND STRUCTURAL MOTIF FOR RECOGNITION OF DNA BY OLIGONUCLEOTIDE-DIRECTED TRIPLE-HELIX FORMATION [J].

BEAL, PA ;

DERVAN, PB .

SCIENCE, 1991, 251 (4999) :1360-1363

[5] DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].

BECKE, AD .

JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652

[6] DENSITY-FUNCTIONAL EXCHANGE-ENERGY APPROXIMATION WITH CORRECT ASYMPTOTIC-BEHAVIOR [J].

BECKE, AD .

PHYSICAL REVIEW A, 1988, 38 (06) :3098-3100

[7] Fundamental aspects of the nucleic acid i-motif structures [J].

Benabou, S. ;

Avino, A. ;

Eritja, R. ;

Gonzalez, C. ;

Gargallo, R. .

RSC ADVANCES, 2014, 4 (51) :26956-26980

[8] Triplex-forming oligonucleotides - Sequence-specific DNA ligands as tools for gene inhibition and for modulation of DNA-associated functions [J].

Besch, R ;

Giovannangeli, C ;

Degitz, K .

CURRENT DRUG TARGETS, 2004, 5 (08) :691-703

[9] Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes [J].

Bikard, David ;

Loot, Celine ;

Baharoglu, Zeynep ;

Mazel, Didier .

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 2010, 74 (04) :570-588

[10] A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].

CORNELL, WD ;

CIEPLAK, P ;

BAYLY, CI ;

GOULD, IR ;

MERZ, KM ;

FERGUSON, DM ;

SPELLMEYER, DC ;

FOX, T ;

CALDWELL, JW ;

KOLLMAN, PA .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197

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