Fundamental Interactions in RNA: Questions Answered and Remaining

被引:12
作者
Turner, Douglas H. [1 ,2 ]
机构
[1] Univ Rochester, Dept Chem, Rochester, NY 14627 USA
[2] Univ Rochester, Ctr RNA Biol, Rochester, NY 14627 USA
关键词
thermodynamics; RNA; stacking; hydrogen bonding; molecular dynamics; NEAREST-NEIGHBOR MODEL; SELF-COMPLEMENTARY OLIGORIBONUCLEOTIDES; FREE-ENERGY CHANGES; SECONDARY STRUCTURE; INTERNAL LOOPS; THERMODYNAMIC STABILITIES; 2-DIMENSIONAL NMR; BASE-PAIRS; ELECTROSTATIC PROPERTIES; CHEMICAL-MODIFICATION;
D O I
10.1002/bip.22294
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
Interpreting the tsunami of sequence information for RNA would be facilitated by an understanding of all the physical principles determining RNA structure. In principle, a complete understanding would make it computationally possible to find RNA sequences that fold for function and to predict their three-dimensional structure. It would, thus, also facilitate discovery of new principles relating structure to function. This review covers some of the progress in understanding RNA over roughly the preceding 40 years and suggests progress still to be made. (c) 2013 Wiley Periodicals, Inc. Biopolymers 99: 1097-1104, 2013.
引用
收藏
页码:1097 / 1104
页数:8
相关论文
共 103 条
[81]   SELF-COMPLEMENTARY OLIGORIBONUCLEOTIDES - EFFECTS OF HELIX DEFECTS AND GUANYLIC ACID-CYTIDYLIC ACID BASE PAIRS [J].
UHLENBECK, OC ;
MARTIN, FH ;
DOTY, P .
JOURNAL OF MOLECULAR BIOLOGY, 1971, 57 (02) :217-+
[82]   EQUIMOLAR ADDITION OF OLIGORIBONUCLEOTIDES WITH T4 RNA LIGASE [J].
UHLENBECK, OC ;
CAMERON, V .
NUCLEIC ACIDS RESEARCH, 1977, 4 (01) :85-98
[83]   AUTOMATED CHEMICAL SYNTHESIS OF LONG OLIGORIBONUCLEOTIDES USING 2'-O-SILYLATED RIBONUCLEOSIDE 3'-O-PHOSPHORAMIDITES ON A CONTROLLED-PORE GLASS SUPPORT - SYNTHESIS OF A 43-NUCLEOTIDE SEQUENCE SIMILAR TO THE 3'-HALF MOLECULE OF AN ESCHERICHIA-COLI FORMYLMETHIONINE TRANSFER-RNA [J].
USMAN, N ;
OGILVIE, KK ;
JIANG, MY ;
CEDERGREN, RJ .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1987, 109 (25) :7845-7854
[84]   Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change [J].
Uzilov, Andrew V. ;
Keegan, Joshua M. ;
Mathews, David H. .
BMC BIOINFORMATICS, 2006, 7 (1)
[85]   Sequence context dependence of tandem Guanine:Adenine mismatch conformations in RNA:: A continuum solvent analysis [J].
Villescas-Diaz, G ;
Zacharias, M .
BIOPHYSICAL JOURNAL, 2003, 85 (01) :416-425
[86]   THE STABILITY AND STRUCTURE OF TANDEM GA MISMATCHES IN RNA DEPEND ON CLOSING BASE-PAIRS [J].
WALTER, AE ;
WU, M ;
TURNER, DH .
BIOCHEMISTRY, 1994, 33 (37) :11349-11354
[87]   Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome [J].
Washietl, S ;
Hofacker, IL ;
Lukasser, M ;
Hüttenhofer, A ;
Stadler, PF .
NATURE BIOTECHNOLOGY, 2005, 23 (11) :1383-1390
[88]   Fast and reliable prediction of noncoding RNAs [J].
Washietl, S ;
Hofacker, IL ;
Stadler, PF .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (07) :2454-2459
[89]   RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction [J].
Washietl, Stefan ;
Hofacker, Ivo L. ;
Stadler, Peter F. ;
Kellis, Manolis .
NUCLEIC ACIDS RESEARCH, 2012, 40 (10) :4261-4272
[90]   RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences [J].
Wei, Donglai ;
Alpert, Lauren V. ;
Lawrence, Charles E. .
BIOINFORMATICS, 2011, 27 (18) :2486-2493