Compacton-like modes in model DNA systems and their bearing on biological functioning

被引：28

作者：

Takeno, S ^{[1
]}

机构：

[1] Nagasaki Inst Appl Sci, Inst Innovat Sci & Technol, Nagasaki 8510193, Japan

来源：

PHYSICS LETTERS A | 2005年 / 339卷 / 3-5期

关键词：

helical structure; sine-plus-linear-lattice model; base pair twisting; compacton-like modes; local open structure; biological functioning;

D O I：

10.1016/j.physleta.2005.01.081

中图分类号：

O4 [物理学];

学科分类号：

0702 ;

摘要：

Existence of non-breathing compacton-like modes considered to be a good candidate for open states in DNA is shown by numerical calculations. This is done by employing an extended version of a coupled sine-plus-linear-lattice model to take care of its helical structure in which the effect of hindered rotation is included in on-site potential energy. (c) 2005 Elsevier B.V. All rights reserved.

引用

页码：352 / 360

页数：9

共 21 条

[1] Spontaneous base flipping in DNA and its possible role in methyltransferase binding [J].

Chen, YZ ;

Mohan, V ;

Griffey, RH .

PHYSICAL REVIEW E, 2000, 62 (01) :1133-1137

[2] DYNAMICS AND THERMODYNAMICS OF A NONLINEAR MODEL FOR DNA DENATURATION [J].

DAUXOIS, T ;

PEYRARD, M ;

BISHOP, AR .

PHYSICAL REVIEW E, 1993, 47 (01) :684-695

[3]

DEVOE H, 1962, J MOL BIOL, V4, P500

[4]

Dodd R. K., 1982, Solitons and nonlinear wave equations

[5] NATURE OF THE OPEN STATE IN LONG POLYNUCLEOTIDE DOUBLE HELICES - POSSIBILITY OF SOLITON EXCITATIONS [J].

ENGLANDER, SW ;

KALLENBACH, NR ;

HEEGER, AJ ;

KRUMHANSL, JA ;

LITWIN, S .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES, 1980, 77 (12) :7222-7226

[6] NONLINEAR DYNAMICS IN A DOUBLE-CHAIN MODEL OF DNA [J].

FORINASH, K ;

BISHOP, AR ;

LOMDAHL, PS .

PHYSICAL REVIEW B, 1991, 43 (13) :10743-10750

[7] MOLECULAR-ORBITAL STUDY OF STABILITY AND CONFORMATION OF DOUBLE-STRANDED DNA-LIKE POLYMERS [J].

FUJITA, H ;

IMAMURA, A ;

NAGATA, C .

JOURNAL OF THEORETICAL BIOLOGY, 1974, 45 (02) :411-433

[8] SINE-LATTICE EQUATION .3. NEARLY INTEGRABLE KINKS WITH ARBITRARY KINK AMPLITUDE [J].

HOMMA, S ;

TAKENO, S .

JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 1987, 56 (10) :3480-3490

[9] A COUPLED BASE-ROTATOR MODEL FOR STRUCTURE AND DYNAMICS OF DNA - LOCAL FLUCTUATIONS IN HELICAL TWIST ANGLES AND TOPOLOGICAL SOLITONS [J].

HOMMA, S ;

TAKENO, S .

PROGRESS OF THEORETICAL PHYSICS, 1984, 72 (04) :679-693

[10] Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes [J].

OGara, M ;

Klimasauskas, S ;

Roberts, RJ ;

Cheng, XD .

JOURNAL OF MOLECULAR BIOLOGY, 1996, 261 (05) :634-645

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