Study of RNA structures with a connection to random matrix theory

Chaos, Solitons and Fractals

Volumn 81, Issue , 2015, Pages 542-550

  Bhadola, Pradeep ^a   Deo, Nivedita ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

Database; Penner interaction; RNA base pairs; RNA structures; RNA thermodynamics random matrix model

Indexed keywords

DATABASE SYSTEMS; FREE ENERGY; HYDROGEN BONDS; MATRIX ALGEBRA; RANDOM VARIABLES; SPECIFIC HEAT; THERMOANALYSIS; THERMODYNAMIC PROPERTIES; THERMODYNAMICS;

BASE PAIRS; NONLINEAR INTERACTIONS; PENNER INTERACTION; RANDOM MATRIX MODEL; RNA STRUCTURES; STRUCTURAL INFORMATION; THERMO DYNAMIC ANALYSIS; THERMODYNAMICAL PROPERTIES;

RNA;

EID: 84948583277     PISSN: 09600779     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chaos.2015.09.005     Document Type: Article

References (23)

1. Lohse P.A., Szostak J.W. Ribozyme-catalysed amino-acid transfer reactions Nature 381 1996 442
2. Unrau P.J., Bartel D.P. RNA-catalysed nucleotide synthesis Nature 395 1998 260
3. Werstuck G., Green M.R. Controlling gene expression in living cells through small molecule-RNA interactions Science 282 1998 296
4. Hatfield S.D., Shcherbata1 H.R., Fischer1 K.A., Nakahara K., Carthew R.W., Baker H.R. Stem cell division is regulated by the microRNA pathway Nature 435 2005 974
5. Waterman M.S. Combinatorics of RNA hairpins and cloverleaves Stud Appl Math 60 1979 91
6. Akutsu T. Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots Discret Appl Math 104 2000 45
7. Hofacker I.L., Fekete M., Stadler P.F. Secondary structure prediction for aligned RNA sequences J Mol Biol 319 2002 1059
8. Haslinger C., Stadler P.F. RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties Bull. Math. Biol. 61 1999 437
9. Jin E.Y., Reidys C.M. Combinatorics of RNA structures with pseudoknots Bull Math Biol 70 2008 45
10. Yang H., Jossinet F., Leontis N., Chen L., Westbrook J., Berman H.M. et al. Tools for the automatic identification and classification of RNA base pairs Nucleic Acids Res 31 13 2003 3450
11. 't Hooft G. A planar diagram theory for stronginteractions Nucl Phys B 72 1974 461
12. Bon M., Vernizzi G., Orland H., Zee A. Topological classification of RNA structures J Mol Biol 379 2008 900
13. Wuchty S., Fontana W., Hofacker I., Schuster P. Complete suboptimal folding of RNA and the stability of secondary structures Biopolymers 49 1999 145
14. Matthews D., Sabina J., Zuker M., Turner D. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J Mol Biol 288 1999 911
15. Mathews D.H., Disney M.D., Childs J.L., Schroeder S.J., Zuker M., Turner D.H. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure Proc Natl Acad Sci USA 101 19 2004 7287
16. R. Lorenz, S.H. Bernhart, C.H. Zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler et al. ViennaRNA Package 2.0 Algorithms for Molecular Biology 6 1 2011 26
17. E.P. Nawrocki, S.W. Burge, A. Bateman, J. Daub, R.Y. Eberhardt, S.R. Eddy et al. Rfam 12.0: updates to the RNA families database Nucleic Acids Res. 2014 10.1093/nar/gku1063
18. Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer S., Tacker M., Schuster P. Fast Folding and Comparison of RNA Secondary Structures Monatsh Chem 125 1994 167
19. Orland H., Zee A. RNA folding and large N matrix theory Nucl Phys B 620 2002 456
20. Vernizzi G., Orland H., Zee A. Enumeration of RNA structures by matrix models Phys Rev Lett 94 2005 168103
21. Bhadola P., Garg I., Deo N. Structure combinatorics and thermodynamics of a matrix model with Penner interaction inspired by interacting RNA Nucl Phys B 870 2013 384
22. Bhadola P., Deo N. Genus distribution and thermodynamics of a random matrix model of RNA with Penner interaction Phys Rev E 88 3 2013 032706
23. Bhadola P., Deo N. Matrix models with Penner interaction inspired by interacting ribonucleic acid Pramana 84(2) 2015 295