Predicting secondary structural folding kinetics for nucleic acids.
We report a new computational approach to the prediction of RNA secondary structure folding kinetics. In this approach, each elementary kinetic step is represented as the transformation between two secondary structures that differ by a helix. Based on the free energy landscape analysis, we identify three types of dominant pathways and the rate constants for the kinetic steps: 1), formation; 2), disruption of a helix stem; and 3), helix formation with concomitant partial melting of a competing (incompatible) helix. The third pathway, termed the tunneling pathway, is the low-barrier dominant pathway for the conversion between two incompatible helices. Comparisons with experimental data indicate that this new method is quite reliable in predicting the kinetics for RNA secondary structural folding and structural rearrangements. The approach presented here may provide a robust first step for further systematic development of a predictive theory for the folding kinetics for large RNAs.
Zhao
Peinan
P
Department of Physics, Wuhan University, Wuhan, China.
Zhang
Wen-Bing
WB
Chen
Shi-Jie
SJ
D001483:Base Sequence; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
D009696:Nucleic Acids
Chembiochem. 2003 Oct 6;4(10):1024-32
14523920
Curr Opin Microbiol. 2007 Apr;10(2):117-24
17376733
Nucleic Acids Res. 2006 Jul 19;34(12):3568-76
16855293
J Biomol Struct Dyn. 1985 Feb;2(5):953-62
2477031
Science. 2001 Apr 27;292(5517):733-7
11326101
RNA. 1995 Mar;1(1):4-6
7489487
J Bioinform Comput Biol. 2006 Apr;4(2):589-96
16819804
Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):1931-6
11842187
J Mol Biol. 1999 Oct 22;293(2):271-81
10550208
Cell Mol Life Sci. 2000 May;57(5):796-808
10892344
Biophys J. 2003 Aug;85(2):790-803
12885628
Science. 2000 Jul 21;289(5478):448-52
10903205
Nature. 2004 Mar 18;428(6980):281-6
15029187
Cell. 2002 Nov 27;111(5):747-56
12464185
J Mol Biol. 2003 May 16;328(5):1011-26
12729738
Biochemistry. 1982 Sep 14;21(19):4734-40
7138823
Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6515-20
10823910
J Am Chem Soc. 2008 Jun 11;130(23):7364-72
18479134
Trends Biochem Sci. 2004 Jan;29(1):11-7
14729327
Chembiochem. 2003 Oct 6;4(10):984-90
14523915
J Mol Biol. 1998 Jun 5;279(2):361-73
9642043
Nano Lett. 2006 Jan;6(1):101-4
16402795
J Mol Biol. 1995 Jun 30;250(1):37-51
7541471
Chem Biol. 2002 Sep;9(9):1043
12323379
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15310-5
14676318
Science. 1990 Aug 3;249(4968):505-10
2200121
J Mol Biol. 1982 Feb 5;154(4):629-48
7086897
J Mol Biol. 1996 Jan 12;255(1):254-66
8568872
Proc Natl Acad Sci U S A. 2001 May 8;98(10):5584-9
11320222
Methods Enzymol. 1995;259:242-61
8538457
EMBO J. 1997 Feb 3;16(3):599-610
9034342
Eur Phys J E Soft Matter. 2003 Dec;12(4):605-15
15007758
RNA. 1999 Nov;5(11):1408-18
10580469
Curr Opin Struct Biol. 2003 Jun;13(3):309-16
12831881
Curr Opin Struct Biol. 2001 Jun;11(3):309-14
11406379
Nature. 1990 Aug 30;346(6287):818-22
1697402
Nat Rev Genet. 2004 Jul;5(7):522-31
15211354
Biopolymers. 2007 Aug 5-15;86(5-6):360-83
17595685
EMBO J. 1992 Dec;11(13):5129-35
1281452
Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8602-6
9671724
Biochemistry. 1995 Jan 31;34(4):1261-6
7530049
Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):646-51
10639133
J Mol Biol. 2002 Apr 5;317(4):493-506
11955005
J Am Chem Soc. 2008 Oct 29;130(43):14080-1
18828635
J Comput Biol. 2005 Jul-Aug;12(6):862-81
16108722
Curr Opin Struct Biol. 2002 Oct;12(5):648-53
12464318
Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):37-41
11120885
RNA. 2000 Mar;6(3):325-38
10744018
Cell. 1982 Nov;31(1):147-57
6297745
J Mol Biol. 2008 May 23;379(1):160-73
18440024
Annu Rev Biophys Biomol Struct. 2006;35:161-75
16689632
Gene. 1989 Oct 15;82(1):83-7
2684778
Science. 1993 Sep 10;261(5127):1411-8
7690155
Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7771-6
11438730
Annu Rev Biophys Biomol Struct. 1997;26:113-37
9241415
Cell. 2004 Jan 23;116(2):281-97
14744438
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):323-34
6198621
Biophys J. 2006 Feb 1;90(3):765-77
16272440
Annu Rev Phys Chem. 2001;52:751-62
11326079
Annu Rev Biophys. 2008;37:197-214
18573079