Calculating nucleic acid secondary structure

被引：188

作者：

Zuker, M ^{[1
]}

机构：

[1] Washington Univ, Dept Biochem & Mol Biophys, St Louis, MO 63110 USA

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2000年 / 10卷 / 03期

关键词：

D O I：

10.1016/S0959-440X(00)00088-9

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：

New results for calculating nucleic acid secondary structure by free energy minimization and phylogenetic comparisons have recently been reported. A complete set of DNA energy parameters is now available and the RNA parameters have been improved. Although databases of RNA secondary structures are still derived and expanded using computer-assisted, ad hoc comparative analysis, a number of new computer algorithms combine covariation analysis with energy methods.

引用

页码：303 / 310

页数：8

共 122 条

[1] Nearest-neighbor thermodynamics of internal A•C mismatches in DNA:: Sequence dependence and pH effects [J].

Allawi, HT ;

SantaLucia, J .

BIOCHEMISTRY, 1998, 37 (26) :9435-9444

[2] Nearest neighbor thermodynamic parameters for internal G•A mismatches in DNA [J].

Allawi, HT ;

SantaLucia, J .

BIOCHEMISTRY, 1998, 37 (08) :2170-2179

[3] Thermodynamics and NMR of internal GT mismatches in DNA [J].

Allawi, HT ;

SantaLucia, J .

BIOCHEMISTRY, 1997, 36 (34) :10581-10594

[4] Thermodynamics of internal C•T mismatches in DNA [J].

Allawi, HT ;

Santalucia, J .

NUCLEIC ACIDS RESEARCH, 1998, 26 (11) :2694-2701

[5] Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling [J].

Babin, P ;

Dolan, M ;

Wollenzien, P ;

Gutell, RR .

RNA, 1999, 5 (11) :1430-1439

[6] Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin [J].

Bevilacqua, JM ;

Bevilacqua, PC .

BIOCHEMISTRY, 1998, 37 (45) :15877-15884

[7] Kinetics of conformational fluctuations in DNA hairpin-loops [J].

Bonnet, G ;

Krichevsky, O ;

Libchaber, A .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (15) :8602-8606

[8] STABILITY OF RIBONUCLEIC-ACID DOUBLE-STRANDED HELICES [J].

BORER, PN ;

DENGLER, B ;

TINOCO, I ;

UHLENBECK, OC .

JOURNAL OF MOLECULAR BIOLOGY, 1974, 86 (04) :843-853

[9] PREDICTING DNA DUPLEX STABILITY FROM THE BASE SEQUENCE [J].

BRESLAUER, KJ ;

FRANK, R ;

BLOCKER, H ;

MARKY, LA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1986, 83 (11) :3746-3750

[10] Prediction of sequentially optimal RNA secondary structures [J].

Breton, N ;

Jacob, C ;

Daegelen, P .

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 1997, 14 (06) :727-740

← 1 2 3 4 5 6 7 8 9 10 →