Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena

被引：121

作者：

Munteanu, MG

Vlahovicek, K

Parthasarathy, S

Simon, I

Pongor, S

机构：

[1] Int Ctr Genet Engn & Biotechnol, I-34012 Trieste, Italy

[2] Hungarian Acad Sci, Inst Enzymol, BRC, H-1518 Budapest, Hungary

来源：

TRENDS IN BIOCHEMICAL SCIENCES | 1998年 / 23卷 / 09期

基金：

匈牙利科学研究基金会;

关键词：

D O I：

10.1016/S0968-0004(98)01265-1

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：

Local bending phenomena can be predicted by elastic models that incorporate sequence-dependent anisotropic-bendability (SDAB). SDAB models consider DNA to be an initially straight, segmented, elastic rod, in which the flexibility of each segment is greater towards the major groove than it is in other directions. While local bending can be predicted by static-geometry models as well, SDAB models, in addition, qualitatively explain such phenomena as the affinity of protein binding and kinking. A set of prediction tools is available at http://www.icgeb.trieste.it/dna.

引用

收藏

页码：341 / 347

页数：7

相关论文

共 40 条

[21] Kinked DNA [J].

Han, WH ;

Lindsay, SM ;

Dlakic, M ;

Harington, RE .

NATURE, 1997, 386 (6625) :563-563

[22] DNA supercoiling, localized bending and thermal fluctuations [J].

Langowski, J ;

Olson, WK ;

Pedersen, SC ;

Tobias, I ;

Westcott, TP ;

Yang, Y .

TRENDS IN BIOCHEMICAL SCIENCES, 1996, 21 (02) :50-50

[23] Structural analysis of mouse rDNA: Coincidence between nuclease hypersensitive sites, DNA curvature and regulatory elements in the intergenic spacer [J].

Langst, G ;

Schatz, T ;

Langowski, J ;

Grummt, I .

NUCLEIC ACIDS RESEARCH, 1997, 25 (03) :511-517

[24] Structure and conformation of helical nucleic acids: Rebuilding program (SCHNArP) [J].

Lu, XJ ;

ElHassan, MA ;

Hunter, CA .

JOURNAL OF MOLECULAR BIOLOGY, 1997, 273 (03) :681-691

[25] FLEXING AND FOLDING DOUBLE-HELICAL DNA [J].

OLSON, WK ;

BABCOCK, MS ;

GORIN, A ;

LIU, GH ;

MARKY, NL ;

MARTINO, JA ;

PEDERSEN, SC ;

SRINIVASAN, AR ;

TOBIAS, I ;

WESTCOTT, TP ;

ZHANG, PS .

BIOPHYSICAL CHEMISTRY, 1995, 55 (1-2) :7-29

[26] Simulating DNA at low resolution [J].

Olson, WK .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 1996, 6 (02) :242-256

[27] INFLUENCE OF FLUCTUATIONS ON DNA CURVATURE - A COMPARISON OF FLEXIBLE AND STATIC WEDGE MODELS OF INTRINSICALLY BENT DNA [J].

OLSON, WK ;

MARKY, NL ;

JERNIGAN, RL ;

ZHURKIN, VB .

JOURNAL OF MOLECULAR BIOLOGY, 1993, 232 (02) :530-551

[28] ACTION AT A DISTANCE - DNA-LOOPING AND INITIATION OF TRANSCRIPTION [J].

RIPPE, K ;

VONHIPPEL, PH ;

LANGOWSKI, J .

TRENDS IN BIOCHEMICAL SCIENCES, 1995, 20 (12) :500-506

[29] Molecular modelling of (A(4)T(4)NN)(n) and (T(4)A(4)NN)(n): Sequence elements responsible for curvature [J].

Sanghani, SR ;

Zakrzewska, K ;

Harvey, SC ;

Lavery, R .

NUCLEIC ACIDS RESEARCH, 1996, 24 (09) :1632-1637

[30] Curvature and sequence analysis of eukaryotic promoters [J].

Schatz, T ;

Langowski, J .

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 1997, 15 (02) :265-275

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