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
[1]  
Afonin KA, 2010, NAT NANOTECHNOL, V5, P676, DOI [10.1038/NNANO.2010.160, 10.1038/nnano.2010.160]
[2]  
ANDERSON CF, 1995, ANNU REV PHYS CHEM, V46, P657, DOI 10.1146/annurev.physchem.46.1.657
[3]  
Atkins J.F., 2011, RNA WORLDS LIFES ORI
[4]   RNAalifold: improved consensus structure prediction for RNA alignments [J].
Bernhart, Stephan H. ;
Hofacker, Ivo L. ;
Will, Sebastian ;
Gruber, Andreas R. ;
Stadler, Peter F. .
BMC BIOINFORMATICS, 2008, 9 (1)
[5]   Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].
Birney, Ewan ;
Stamatoyannopoulos, John A. ;
Dutta, Anindya ;
Guigo, Roderic ;
Gingeras, Thomas R. ;
Margulies, Elliott H. ;
Weng, Zhiping ;
Snyder, Michael ;
Dermitzakis, Emmanouil T. ;
Stamatoyannopoulos, John A. ;
Thurman, Robert E. ;
Kuehn, Michael S. ;
Taylor, Christopher M. ;
Neph, Shane ;
Koch, Christoph M. ;
Asthana, Saurabh ;
Malhotra, Ankit ;
Adzhubei, Ivan ;
Greenbaum, Jason A. ;
Andrews, Robert M. ;
Flicek, Paul ;
Boyle, Patrick J. ;
Cao, Hua ;
Carter, Nigel P. ;
Clelland, Gayle K. ;
Davis, Sean ;
Day, Nathan ;
Dhami, Pawandeep ;
Dillon, Shane C. ;
Dorschner, Michael O. ;
Fiegler, Heike ;
Giresi, Paul G. ;
Goldy, Jeff ;
Hawrylycz, Michael ;
Haydock, Andrew ;
Humbert, Richard ;
James, Keith D. ;
Johnson, Brett E. ;
Johnson, Ericka M. ;
Frum, Tristan T. ;
Rosenzweig, Elizabeth R. ;
Karnani, Neerja ;
Lee, Kirsten ;
Lefebvre, Gregory C. ;
Navas, Patrick A. ;
Neri, Fidencio ;
Parker, Stephen C. J. ;
Sabo, Peter J. ;
Sandstrom, Richard ;
Shafer, Anthony .
NATURE, 2007, 447 (7146) :799-816
[6]   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
[7]   Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs [J].
Burkard, ME ;
Kierzek, R ;
Turner, DH .
JOURNAL OF MOLECULAR BIOLOGY, 1999, 290 (05) :967-982
[9]   Stacking effects on local structure in RNA: Changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs [J].
Chen, Gang ;
Kierzek, Ryszard ;
Yildirim, Ilyas ;
Krugh, Thomas R. ;
Turner, Douglas H. ;
Kennedy, Scott D. .
JOURNAL OF PHYSICAL CHEMISTRY B, 2007, 111 (24) :6718-6727
[10]   Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters [J].
Chen, Jonathan L. ;
Dishler, Abigael L. ;
Kennedy, Scott D. ;
Yildirim, Ilyas ;
Liu, Biao ;
Turner, Douglas H. ;
Serra, Martin J. .
BIOCHEMISTRY, 2012, 51 (16) :3508-3522