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Volumn 109, Issue 6, 2012, Pages

Transition path times for nucleic acid folding determined from energy-landscape analysis of single-molecule trajectories

(6) Neupane, Krishna a Ritchie, Dustin B a Yu, Hao a Foster, Daniel A N a Wang, Feng b Woodside, Michael T a,b

a UNIVERSITY OF ALBERTA (Canada)

b NATIONAL RESEARCH COUNCIL CANADA (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CONFIGURATIONAL ENERGY; CRITICAL EVENTS; DIFFUSION CONSTANT; DNA HAIRPIN; ENERGY LANDSCAPE; FOLDING REACTIONS; OPTICAL TRAP; PSEUDO-KNOTS; RIBOSWITCHES; RNA FOLDING; SINGLE-MOLECULE; STRUCTURAL TRANSITIONS; TIME SPENT; TRANSITION PATHS; TRANSITION TIME;

BIOPOLYMERS; RNA;

MOLECULES;

EID: 84864661883 PISSN: 00319007 EISSN: 10797114 Source Type: Journal
DOI: 10.1103/PhysRevLett.109.068102 Document Type: Article

Times cited : (115)

References (31)

1
- 84889863672
- Wiley-VCH, Weinheim
- J. Buchner and T. Kiefhaber, Protein Folding Handbook (Wiley-VCH, Weinheim, 2005).
- (2005) Protein Folding Handbook
- Buchner, J.¹ Kiefhaber, T.²

2
- 50649092124
- ARBOAW 0066-4154 10.1146/annurev.biochem.77.060706.093102
- A. Borgia, P.M. Williams, and J. Clarke, Annu. Rev. Biochem. 77, 101 (2008). ARBOAW 0066-4154 10.1146/annurev.biochem.77.060706.093102
- (2008) Annu. Rev. Biochem. , vol.77 , pp. 101
- Borgia, A.¹ Williams, P.M.² Clarke, J.³

3
- 57549107708
- COCBF4 1367-5931 10.1016/j.cbpa.2008.08.011
- M.T. Woodside, C. Garcia-Garcia, and S.M. Block, Curr. Opin. Chem. Biol. 12, 640 (2008). COCBF4 1367-5931 10.1016/j.cbpa.2008.08.011
- (2008) Curr. Opin. Chem. Biol. , vol.12 , pp. 640
- Woodside, M.T.¹ Garcia-Garcia, C.² Block, S.M.³

4
- 16344371778
- RNA and protein folding: Common themes and variations
- DOI 10.1021/bi047314+
- D. Thirumalai and C. Hyeon, Biochemistry BICHAW 0006-2960 44, 4957 (2005). 10.1021/bi047314+ (Pubitemid 40471212)
- (2005) Biochemistry , vol.44 , Issue.13 , pp. 4957-4970
- Thirumalai, D.¹ Hyeon, C.²

5
- 34247589224
- Measuring the folding transition time of single RNA molecules
- DOI 10.1529/biophysj.106.094623
- T.-H. Lee, L.J. Lapidus, W. Zhao, K.J. Travers, D. Herschlag, and S. Chu, Biophys. J. 92, 3275 (2007). BIOJAU 0006-3495 10.1529/biophysj.106.094623 (Pubitemid 46684586)
- (2007) Biophysical Journal , vol.92 , Issue.9 , pp. 3275-3283
- Lee, T.-H.¹ Lapidus, L.J.² Zhao, W.³ Travers, K.J.⁴ Herschlag, D.⁵ Chu, S.⁶

6
- 67749147584
- PNASA6 0027-8424 10.1073/pnas.0901178106
- H.S. Chung, J.M. Louis, and W.A. Eaton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 106, 11837 (2009). 10.1073/pnas.0901178106
- (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 11837
- Chung, H.S.¹ Louis, J.M.² Eaton, W.A.³

7
- 84857510185
- SCIEAS 0036-8075 10.1126/science.1215768
- H.S. Chung, K. McHale, J.M. Louis, and W.A. Eaton, Science 335, 981 (2012). SCIEAS 0036-8075 10.1126/science.1215768
- (2012) Science , vol.335 , pp. 981
- Chung, H.S.¹ McHale, K.² Louis, J.M.³ Eaton, W.A.⁴

8
- 84857033265
- COSBEF 0959-440X 10.1016/j.sbi.2011.12.001
- R.B. Best, Curr. Opin. Struct. Biol. 22, 52 (2012). COSBEF 0959-440X 10.1016/j.sbi.2011.12.001
- (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 52
- Best, R.B.¹

9
- 33747592347
- The experimental survey of protein-folding energy landscapes
- DOI 10.1017/S0033583506004185, PII S0033583506004185
- M. Oliveberg and P.G. Wolynes, Q. Rev. Biophys. QURBAW 0033-5835 38, 245 (2005). 10.1017/S0033583506004185 (Pubitemid 44268537)
- (2005) Quarterly Reviews of Biophysics , vol.38 , Issue.3 , pp. 245-288
- Oliveberg, M.¹ Wolynes, P.G.²

10
- 0347193736
- RMPHAT 0034-6861 10.1103/RevModPhys.62.251
- P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. 62, 251 (1990). RMPHAT 0034-6861 10.1103/RevModPhys.62.251
- (1990) Rev. Mod. Phys. , vol.62 , pp. 251
- Hänggi, P.¹ Talkner, P.² Borkovec, M.³

11
- 0842311640
- JCPSA6 0021-9606 10.1063/1.1630572
- G. Hummer, J. Chem. Phys. 120, 516 (2004). JCPSA6 0021-9606 10.1063/1.1630572
- (2004) J. Chem. Phys. , vol.120 , pp. 516
- Hummer, G.¹

12
- 1342281633
- The protein folding 'speed limit'
- DOI 10.1016/j.sbi.2004.01.013
- J. Kubelka, J. Hofrichter, and W.A. Eaton, Curr. Opin. Struct. Biol. 14, 76 (2004). COSBEF 0959-440X 10.1016/j.sbi.2004.01.013 (Pubitemid 38249596)
- (2004) Current Opinion in Structural Biology , vol.14 , Issue.1 , pp. 76-88
- Kubelka, J.¹ Hofrichter, J.² Eaton, W.A.³

13
- 33750970551
- Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
- DOI 10.1126/science.1133601
- M.T. Woodside, P.C. Anthony, W.M. Behnke-Parks, K. Larizadeh, D. Herschlag, and S.M. Block, Science 314, 1001 (2006). SCIEAS 0036-8075 10.1126/science.1133601 (Pubitemid 44749947)
- (2006) Science , vol.314 , Issue.5801 , pp. 1001-1004
- Woodside, M.T.¹ Anthony, P.C.² Behnke-Parks, W.M.³ Larizadeh, K.⁴ Herschlag, D.⁵ Block, S.M.⁶

14
- 0035957434
- Free energy reconstruction from nonequilibrium single-molecule pulling experiments
- DOI 10.1073/pnas.071034098
- G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 98, 3658 (2001). 10.1073/pnas.071034098 (Pubitemid 32249826)
- (2001) Proceedings of the National Academy of Sciences of the United States of America , vol.98 , Issue.7 , pp. 3658-3661
- Hummer, G.¹ Szabo, A.²

15
- 79961021741
- NPAHAX 1745-2473 10.1038/nphys2022
- A.N. Gupta, A. Vincent, K. Neupane, H. Yu, F. Wang, and M.T. Woodside, Nature Phys. NPAHAX 1745-2473 7, 631 (2011). 10.1038/nphys2022
- (2011) Nature Phys. , vol.7 , pp. 631
- Gupta, A.N.¹ Vincent, A.² Neupane, K.³ Yu, H.⁴ Wang, F.⁵ Woodside, M.T.⁶

16
- 33645004171
- PRLTAO 0031-9007 10.1103/PhysRevLett.96.108101
- O.K. Dudko, G. Hummer, and A. Szabo, Phys. Rev. Lett. 96, 108101 (2006). PRLTAO 0031-9007 10.1103/PhysRevLett.96.108101
- (2006) Phys. Rev. Lett. , vol.96 , pp. 108101
- Dudko, O.K.¹ Hummer, G.² Szabo, A.³

17
- 57349124448
- PNASA6 0027-8424 10.1073/pnas.0806085105
- O.K. Dudko, G. Hummer, and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 105, 15755 (2008). 10.1073/pnas.0806085105
- (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 15755
- Dudko, O.K.¹ Hummer, G.² Szabo, A.³

18
- 80053216036
- NARHAD 0305-1048 10.1093/nar/gkr305
- K. Neupane, H. Yu, D.A.N. Foster, F. Wang, and M.T. Woodside, Nucleic Acids Res. 39, 7677 (2011). NARHAD 0305-1048 10.1093/nar/gkr305
- (2011) Nucleic Acids Res. , vol.39 , pp. 7677
- Neupane, K.¹ Yu, H.² Foster, D.A.N.³ Wang, F.⁴ Woodside, M.T.⁵

19
- 33646587736
- PNASA6 0027-8424 10.1073/pnas.0511048103
- M.T. Woodside, W.M. Behnke-Parks, K. Larizadeh, K. Travers, D. Herschlag, and S.M. Block, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 6190 (2006). 10.1073/pnas.0511048103
- (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 6190
- Woodside, M.T.¹ Behnke-Parks, W.M.² Larizadeh, K.³ Travers, K.⁴ Herschlag, D.⁵ Block, S.M.⁶

20
- 84859465192
- PNASA6 0027-8424 10.1073/pnas.1107736109
- H. Yu, X. Liu, K. Neupane, A.N. Gupta, A.M. Brigley, A. Solanki, S. Iveta, and M.T. Woodside, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 109, 5283 (2012). 10.1073/pnas.1107736109
- (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , pp. 5283
- Yu, H.¹ Liu, X.² Neupane, K.³ Gupta, A.N.⁴ Brigley, A.M.⁵ Solanki, A.⁶ Iveta, S.⁷ Woodside, M.T.⁸

21
- 70350101421
- JPCBFK 1520-6106 10.1021/jp811122a
- T. Kaji, S. Ito, S. Iwai, and H. Miyasaka, J. Phys. Chem. B 113, 13917 (2009). JPCBFK 1520-6106 10.1021/jp811122a
- (2009) J. Phys. Chem. B , vol.113 , pp. 13917
- Kaji, T.¹ Ito, S.² Iwai, S.³ Miyasaka, H.⁴

22
- 0034934258
- Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins
- DOI 10.1073/pnas.131477798
- A. Ansari, S.V. Kuznetsov, and Y. Shen, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 98, 7771 (2001). 10.1073/pnas.131477798 (Pubitemid 32642636)
- (2001) Proceedings of the National Academy of Sciences of the United States of America , vol.98 , Issue.14 , pp. 7771-7776
- Ansari, A.¹ Kuznetsov, S.V.² Shen, Y.³

23
- 1642576003
- Kinetics of End-to-End Collision in Short Single-Stranded Nucleic Acids
- DOI 10.1021/ja038263r
- X. Wang and W.M. Nau, J. Am. Chem. Soc. 126, 808 (2004). JACSAT 0002-7863 10.1021/ja038263r (Pubitemid 38114364)
- (2004) Journal of the American Chemical Society , vol.126 , Issue.3 , pp. 808-813
- Wang, X.¹ Nau, W.M.²

24
- 84864716995
- See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevLett.109.068102 for details on the materials and methods.

25
- 34447538279
- Viral RNA pseudoknots: Versatile motifs in gene expression and replication
- DOI 10.1038/nrmicro1704, PII NRMICRO1704
- I. Brierley, S. Pennell, and R.J.C. Gilbert, Nat. Rev. Microbiol. 5, 598 (2007). 1740-1526 10.1038/nrmicro1704 (Pubitemid 47074115)
- (2007) Nature Reviews Microbiology , vol.5 , Issue.8 , pp. 598-610
- Brierley, I.¹ Pennell, S.² Gilbert, R.J.C.³

26
- 38849204944
- Direct observation of hierarchical folding in single riboswitch aptamers
- DOI 10.1126/science.1151298
- W.J. Greenleaf, K.L. Frieda, D.A.N. Foster, M.T. Woodside, and S.M. Block, Science 319, 630 (2008). SCIEAS 0036-8075 10.1126/science.1151298 (Pubitemid 351197067)
- (2008) Science , vol.319 , Issue.5863 , pp. 630-633
- Greenleaf, W.J.¹ Frieda, K.L.² Foster, D.A.N.³ Woodside, M.T.⁴ Block, S.M.⁵

27
- 0016256162
- BICIAZ 0301-4622 10.1016/0301-4622(74)80029-3
- D. Pörschke, Biophys. Chem. 2, 97 (1974). BICIAZ 0301-4622 10.1016/0301-4622(74)80029-3
- (1974) Biophys. Chem. , vol.2 , pp. 97
- Pörschke, D.¹

28
- 2342470819
- EPJSFH 1292-8941 10.1140/epje/e2003-00019-8
- S. Cocco, J.F. Marko, and R. Monasson, Eur. Phys. J. E EPJSFH 1292-8941 10, 153 (2003). 10.1140/epje/e2003-00019-8
- (2003) Eur. Phys. J. e , vol.10 , pp. 153
- Cocco, S.¹ Marko, J.F.² Monasson, R.³

29
- 84855451687
- BIOJAU 0006-3495 10.1016/j.bpj.2011.11.4017
- S.V. Kuznetsov and A. Ansari, Biophys. J. 102, 101 (2012). BIOJAU 0006-3495 10.1016/j.bpj.2011.11.4017
- (2012) Biophys. J. , vol.102 , pp. 101
- Kuznetsov, S.V.¹ Ansari, A.²

30
- 0034604105
- A surprising simplicity to protein folding
- DOI 10.1038/35011000
- D. Baker, Nature (London) NATUAS 0028-0836 405, 39 (2000). 10.1038/35011000 (Pubitemid 30321807)
- (2000) Nature , vol.405 , Issue.6782 , pp. 39-42
- Baker, D.¹

31
- 0024121530
- Diffusion in a rough potential
- DOI 10.1073/pnas.85.7.2029
- R. Zwanzig, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 85, 2029 (1988). 10.1073/pnas.85.7.2029 (Pubitemid 24315821)
- (1988) Proceedings of the National Academy of Sciences of the United States of America , vol.85 , Issue.7 , pp. 2029-2030
- Zwanzig, R.¹

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