SCOPUS 정보 검색 플랫폼

Volumn 34, Issue 6, 2011, Pages

Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: Implications for DNA hybridization

(3) Einert, T R a Orland, H b Netz, R R a,c

a TECHNICAL UNIVERSITY OF MUNICH (Germany)

b CEA SACLAY (France)

c FREIE UNIVERSITÄT BERLIN (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIRING; BASE PAIRS; CRITICAL EXPONENT; DNA HYBRIDIZATION; DOUBLE STRANDS; EXTERNAL FORCE; FORCE-EXTENSION CURVES; FORCE-INDUCED MELTING; HIGH TEMPERATURE; LOW TEMPERATURES; MELTING TRANSITIONS; PULLING FORCE; RNA MOLECULES; SECONDARY STRUCTURE ELEMENTS; SECONDARY STRUCTURE FORMATION; SECONDARY STRUCTURES; SINGLE MOLECULE FORCE SPECTROSCOPY; SINGULAR BEHAVIOR; THERMODYNAMIC LIMITS; VARYING TEMPERATURE;

DENATURATION; ENTROPY; MELTING; PHASE DIAGRAMS; RNA;

BIOMOLECULES;

DNA; RNA; SINGLE STRANDED DNA;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENTROPY; NUCLEIC ACID HYBRIDIZATION; PHASE TRANSITION; TEMPERATURE; THERMODYNAMICS;

BASE PAIRING; DNA; DNA, SINGLE-STRANDED; ENTROPY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; PHASE TRANSITION; RNA; TEMPERATURE; THERMODYNAMICS;

EID: 79958161548 PISSN: 12928941 EISSN: 1292895X Source Type: Journal
DOI: 10.1140/epje/i2011-11055-2 Document Type: Article

Times cited : (16)

References (48)

1
- 0003604405
- (Editors) , 2nd edn. (Cold Spring Harbor Laboratory Press, Woodbury)
- R.F. Gesteland, T.R. Cech, J.F. Atkins (Editors), The RNA World, 2nd edn. (Cold Spring Harbor Laboratory Press, Woodbury, 2005).
- (2005) The RNA World
- Gesteland, R.F.¹ Cech, T.R.² Atkins, J.F.³

2
- 0030024985
- 1996Sci.271.795S 10.1126/science.271.5250.795
- S.B. Smith Y.J. Cui C. Bustamante 1996 Science 271 795 1996Sci...271..795S 10.1126/science.271.5250.795
- (1996) Science , vol.271 , pp. 795
- Smith, S.B.¹ Cui, Y.J.² Bustamante, C.³

3
- 0037036070
- Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
- DOI 10.1126/science.1071152
- J. Liphardt S. Dumont S.B. Smith I. Tinoco jr. C. Bustamante 2002 Science 296 1832 2002Sci...296.1832L 10.1126/science.1071152 (Pubitemid 34596263)
- (2002) Science , vol.296 , Issue.5574 , pp. 1832-1835
- Liphardt, J.¹ Dumont, S.² Smith, S.B.³ Tinoco Jr., I.⁴ Bustamante, C.⁵

4
- 0032919143
- Sequence-dependent mechanics of single DNA molecules
- DOI 10.1038/7582
- M. Rief H. Clausen-Schaumann H.E. Gaub 1999 Nat. Struct. Biol. 6 346 10.1038/7582 (Pubitemid 29166483)
- (1999) Nature Structural Biology , vol.6 , Issue.4 , pp. 346-349
- Rief, M.¹ Clausen-Schaumann, H.² Gaub, H.E.³

5
- 0034710990
- 2000PNAS.9712002M 10.1073/pnas.97.22.12002
- B. Maier D. Bensimon V. Croquette 2000 Proc. Natl. Acad. Sci. U.S.A. 97 12002 2000PNAS...9712002M 10.1073/pnas.97.22.12002
- (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 12002
- Maier, B.¹ Bensimon, D.² Croquette, V.³

6
- 0001767132
- 1997PhRvL.79.4489B 10.1103/PhysRevLett.79.4489
- U. Bockelmann B. Essevaz-Roulet F. Heslot 1997 Phys. Rev. Lett. 79 4489 1997PhRvL..79.4489B 10.1103/PhysRevLett.79.4489
- (1997) Phys. Rev. Lett. , vol.79 , pp. 4489
- Bockelmann, U.¹ Essevaz-Roulet, B.² Heslot, F.³

7
- 65449174872
- 10.1088/1742-5468/2009/02/P02060
- A. Mossa M. Manosas N. Forns J.M. Huguet F. Ritort 2009 J. Stat. Mech. 2009 P02060 10.1088/1742-5468/2009/02/P02060
- (2009) J. Stat. Mech. , vol.2009 , pp. 02060
- Mossa, A.¹ Manosas, M.² Forns, N.³ Huguet, J.M.⁴ Ritort, F.⁵

8
- 0015216137
- 1971Natur.230.362T 10.1038/230362a0
- I. Tinoco O.C. Uhlenbeck M.D. Levine 1971 Nature 230 362 1971Natur.230..362T 10.1038/230362a0
- (1971) Nature , vol.230 , pp. 362
- Tinoco, I.¹ Uhlenbeck, O.C.² Levine, M.D.³

9
- 0345281589
- How RNA folds
- DOI 10.1006/jmbi.1999.3001
- I. Tinoco jr. C. Bustamante 1999 J. Mol. Biol. 293 271 10.1006/jmbi.1999.3001 (Pubitemid 29516169)
- (1999) Journal of Molecular Biology , vol.293 , Issue.2 , pp. 271-281
- Tinoco Jr., I.¹ Bustamante, C.²

10
- 3042638519
- Physics of protein folding
- DOI 10.1016/j.plrev.2004.03.001
- A.V. Finkelstein O.V. Galzitskaya 2004 Phys. Life Rev. 1 23 2004PhLRv...1...23F 10.1016/j.plrev.2004.03.001 (Pubitemid 38808598)
- (2004) Physics of Life Reviews , vol.1 , Issue.1 , pp. 23-56
- Finkelstein, A.V.¹ Galzitskaya, O.V.²

11
- 0014238951
- 10.1002/bip.1968.360060508
- P.G. de Gennes 1968 Biopolymers 6 715 10.1002/bip.1968.360060508
- (1968) Biopolymers , vol.6 , pp. 715
- De Gennes, P.G.¹

12
- 0018254569
- RNA secondary structure: A complete mathematical analysis
- DOI 10.1016/0025-5564(78)90099-8
- M.S. Waterman T.F. Smith 1978 Math. Biosci. 42 257 0402.92016 10.1016/0025-5564(78)90099-8 (Pubitemid 9119476)
- (1978) Mathematical Biosciences , vol.42 , Issue.3-4 , pp. 257-266
- Waterman, M.S.¹ Smith, T.F.²

13
- 48049112038
- 2008PhRvL.101d8103E 10.1103/PhysRevLett.101.048103
- T.R. Einert P. Näger H. Orland R.R. Netz 2008 Phys. Rev. Lett. 101 048103 2008PhRvL.101d8103E 10.1103/PhysRevLett.101.048103
- (2008) Phys. Rev. Lett. , vol.101 , pp. 048103
- Einert, T.R.¹ Näger, P.² Orland, H.³ Netz, R.R.⁴

14
- 34249772381
- 10.1007/BF00818163
- I.L. Hofacker W. Fontana P.F. Stadler L.S. Bonhoeffer M. Tacker P. Schuster 1994 Mon. Chem. 125 167 10.1007/BF00818163
- (1994) Mon. Chem. , vol.125 , pp. 167
- Hofacker, I.L.¹ Fontana, W.² Stadler, P.F.³ Bonhoeffer, L.S.⁴ Tacker, M.⁵ Schuster, P.⁶

15
- 0025264854
- 10.1002/bip.360290621
- J.S. McCaskill 1990 Biopolymers 29 1105 10.1002/bip.360290621
- (1990) Biopolymers , vol.29 , pp. 1105
- McCaskill, J.S.¹

16
- 77955200084
- 2010BpJ.99.578E 10.1016/j.bpj.2010.04.046
- T.R. Einert D.B. Staple H. Kreuzer R.R. Netz 2010 Biophys. J. 99 578 2010BpJ....99..578E 10.1016/j.bpj.2010.04.046
- (2010) Biophys. J. , vol.99 , pp. 578
- Einert, T.R.¹ Staple, D.B.² Kreuzer, H.³ Netz, R.R.⁴

17
- 6644229670
- Hairpin formation and elongation of biomolecules
- DOI 10.1103/PhysRevLett.86.2178
- A. Montanari M. Mézard 2001 Phys. Rev. Lett. 86 2178 2001PhRvL..86.2178M 10.1103/PhysRevLett.86.2178 (Pubitemid 32254790)
- (2001) Physical Review Letters , vol.86 , Issue.10 , pp. 2178-2181
- Montanari, A.¹ Mezard, M.²

18
- 0034844254
- 10.1016/S0006-3495(01)75789-X
- U. Gerland R. Bundschuh T. Hwa 2001 Biophys. J. 81 1324 10.1016/S0006-3495(01)75789-X
- (2001) Biophys. J. , vol.81 , pp. 1324
- Gerland, U.¹ Bundschuh, R.² Hwa, T.³

19
- 0036769453
- M. Müller F. Krzakala M. Mézard 2002 Eur. Phys. J. E 9 67
- (2002) Eur. Phys. J. e , vol.9 , pp. 67
- Müller, M.¹ Krzakala, F.² Mézard, M.³

20
- 40749116530
- Denaturation transition of stretched DNA
- DOI 10.1103/PhysRevLett.100.018106
- A. Hanke M.G. Ochoa R. Metzler 2008 Phys. Rev. Lett. 100 018106 2008PhRvL.100a8106H 10.1103/PhysRevLett.100.018106 (Pubitemid 351388336)
- (2008) Physical Review Letters , vol.100 , Issue.1 , pp. 018106
- Hanke, A.¹ Ochoa, M.G.² Metzler, R.³

21
- 0038187577
- Theoretical models for single-molecule DNA and RNA experiments: From elasticity to unzipping
- DOI 10.1016/S1631-0705(02)01345-2, PII S1631070502013452
- S. Cocco J.F. Marko R. Monasson 2002 C. R. Phys. 3 569 2002CRPhy...3..569C 10.1016/S1631-0705(02)01345-2 (Pubitemid 36646035)
- (2002) Comptes Rendus Physique , vol.3 , Issue.5 , pp. 569-584
- Cocco, S.¹ Marko, J.F.² Monasson, R.³

22
- 37649027722
- Single molecule statistics and the polynucleotide unzipping transition
- DOI 10.1103/PhysRevE.65.031917, 031917
- D.K. Lubensky D.R. Nelson 2002 Phys. Rev. E 65 031917 2002PhRvE..65c1917L 10.1103/PhysRevE.65.031917 (Pubitemid 40619160)
- (2002) Physical Review E - Statistical, Nonlinear, and Soft Matter Physics , vol.65 , Issue.3
- Lubensky, D.K.¹ Nelson, D.R.²

23
- 28844503373
- Coupled dynamics of RNA folding and nanopore translocation
- DOI 10.1103/PhysRevLett.95.208104, 208104
- R. Bundschuh U. Gerland 2005 Phys. Rev. Lett. 95 208104 2005PhRvL..95t8104B 10.1103/PhysRevLett.95.208104 (Pubitemid 41777163)
- (2005) Physical Review Letters , vol.95 , Issue.20 , pp. 1-4
- Bundschuh, R.¹ Gerland, U.²

24
- 79960294452
- in print
- T.R. Einert, R.R. Netz, Biophys. J., 100 (11), in print (2010).
- (2010) Biophys. J. , vol.100 , Issue.11
- Einert, T.R.¹ Netz, R.R.²

25
- 33645775325
- 2006BpJ.90.1175T 10.1529/biophysj.105.070904
- Z.J. Tan S.J. Chen 2006 Biophys. J. 90 1175 2006BpJ....90.1175T 10.1529/biophysj.105.070904
- (2006) Biophys. J. , vol.90 , pp. 1175
- Tan, Z.J.¹ Chen, S.J.²

26
- 34547294972
- RNA folding in the presence of counterions
- DOI 10.1103/PhysRevE.75.061907
- Y.S. Mamasakhlisov S. Hayryan V.F. Morozov C.K. Hu 2007 Phys. Rev. E 75 061907 2007PhRvE..75f1907M 10.1103/PhysRevE.75.061907 (Pubitemid 47140302)
- (2007) Physical Review E - Statistical, Nonlinear, and Soft Matter Physics , vol.75 , Issue.6 , pp. 061907
- Mamasakhlisov, Y.Sh.¹ Hayryan, S.² Morozov, V.F.³ Hu, C.-K.⁴

27
- 17344386261
- 2003PhRvL.91s8102B 10.1103/PhysRevLett.91.198102
- M. Baiesi E. Orlandini A.L. Stella 2003 Phys. Rev. Lett. 91 198102 2003PhRvL..91s8102B 10.1103/PhysRevLett.91.198102
- (2003) Phys. Rev. Lett. , vol.91 , pp. 198102
- Baiesi, M.¹ Orlandini, E.² Stella, A.L.³

28
- 0942289599
- RNA folding and large N matrix theory
- DOI 10.1016/S0550-3213(01)00522-3, PII S0550321301005223
- H. Orland A. Zee 2002 Nucl. Phys. B 620 456 1877957 2002NuPhB.620..456O 0991.92011 10.1016/S0550-3213(01)00522-3 (Pubitemid 41185530)
- (2002) Nuclear Physics B , vol.620 , Issue.3 , pp. 456-476
- Orland, H.¹ Zee, A.²

29
- 2542485691
- 2003PhRvE.68f1911B 10.1103/PhysRevE.68.061911
- R. Blossey E. Carlon 2003 Phys. Rev. E 68 061911 2003PhRvE..68f1911B 10.1103/PhysRevE.68.061911
- (2003) Phys. Rev. e , vol.68 , pp. 061911
- Blossey, R.¹ Carlon, E.²

30
- 0034351060
- Why is the DNA denaturation transition first order?
- DOI 10.1103/PhysRevLett.85.4988
- Y. Kafri D. Mukamel L. Peliti 2000 Phys. Rev. Lett. 85 4988 2000PhRvL..85.4988K 10.1103/PhysRevLett.85.4988 (Pubitemid 32871686)
- (2000) Physical Review Letters , vol.85 , Issue.23 , pp. 4988-4991
- Kafri, Y.¹ Mukamel, D.² Peliti, L.³

31
- 0003880161
- Garland Science
- B. Alberts, Molecular Biology of the Cell (Garland Science, 2002).
- (2002) Molecular Biology of the Cell
- Alberts, B.¹

32
- 76649093956
- 2010PNAS.107.2013G 10.1073/pnas.0909854107
- J.C.M. Gebhardt T. Bornschlögl M. Rief 2010 Proc. Natl. Acad. Sci. U.S.A. 107 2013 2010PNAS..107.2013G 10.1073/pnas.0909854107
- (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 2013
- Gebhardt, J.C.M.¹ Bornschlögl, T.² Rief, M.³

33
- 0032552882
- Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson - Crick base pairs
- DOI 10.1021/bi9809425
- T. Xia J. SantaLucia jr. M.E. Burkard R. Kierzek S.J. Schroeder X. Jiao C. Cox D.H. Turner 1998 Biochemistry 37 14719 10.1021/bi9809425 (Pubitemid 28487580)
- (1998) Biochemistry , vol.37 , Issue.42 , pp. 14719-14735
- Xia, T.¹ SantaLucia Jr., J.² Burkard, M.E.³ Kierzek, R.⁴ Schroeder, S.J.⁵ Jiao, X.⁶ Cox, C.⁷ Turner, D.H.⁸

34
- 0036740902
- 2002EL.59.903B 10.1209/epl/i2002-00128-3
- R. Bundschuh T. Hwa 2002 Europhys. Lett. 59 903 2002EL.....59..903B 10.1209/epl/i2002-00128-3
- (2002) Europhys. Lett. , vol.59 , pp. 903
- Bundschuh, R.¹ Hwa, T.²

35
- 0003544037
- Cornell University Press
- P.G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, 1979).
- (1979) Scaling Concepts in Polymer Physics
- De Gennes, P.G.¹

36
- 3542992583
- 853268 1986PhRvL.57.941D 10.1103/PhysRevLett.57.941
- B. Duplantier 1986 Phys. Rev. Lett. 57 941 853268 1986PhRvL..57..941D 10.1103/PhysRevLett.57.941
- (1986) Phys. Rev. Lett. , vol.57 , pp. 941
- Duplantier, B.¹

37
- 0038056268
- 1975187 2003PhRvE.67b1914M 10.1103/PhysRevE.67.021914
- M. Müller 2003 Phys. Rev. E 67 021914 1975187 2003PhRvE..67b1914M 10.1103/PhysRevE.67.021914
- (2003) Phys. Rev. e , vol.67 , pp. 021914
- Müller, M.¹

38
- 0003864328
- McGraw-Hill
- A. Erdélyi, Higher Transcendental Functions, Vol. 1 (McGraw-Hill, 1953).
- (1953) Higher Transcendental Functions , vol.1
- Erdélyi, A.¹

39
- 0000640693
- 1039294 0712.05004 10.1137/0403019
- P. Flajolet A. Odlyzko 1990 SIAM Discret. Math. 3 216 1039294 0712.05004 10.1137/0403019
- (1990) SIAM Discret. Math. , vol.3 , pp. 216
- Flajolet, P.¹ Odlyzko, A.²

40
- 0004245694
- (Editors), 10th edn. (U.S. Department of Commerce)
- M. Abramowitz, I.A. Stegun (Editors), Handbook of Mathematical Functions, 10th edn. (U.S. Department of Commerce, 2002).
- (2002) Handbook of Mathematical Functions
- Abramowitz, M.¹ Stegun, I.A.²

41
- 18344386476
- 1999PhRvL.83.1066L 10.1103/PhysRevLett.83.1066
- J.F. Léger G. Romano A. Sarkar J. Robert L. Bourdieu D. Chatenay J.F. Marko 1999 Phys. Rev. Lett. 83 1066 1999PhRvL..83.1066L 10.1103/PhysRevLett.83.1066
- (1999) Phys. Rev. Lett. , vol.83 , pp. 1066
- Léger, J.F.¹ Romano, G.² Sarkar, A.³ Robert, J.⁴ Bourdieu, L.⁵ Chatenay, D.⁶ Marko, J.F.⁷

42
- 0013953695
- 1966JChPh.45.1456P 10.1063/1.1727785
- D. Poland H.A. Scheraga 1966 J. Chem. Phys. 45 1456 1966JChPh..45.1456P 10.1063/1.1727785
- (1966) J. Chem. Phys. , vol.45 , pp. 1456
- Poland, D.¹ Scheraga, H.A.²

43
- 0013952703
- 1966JChPh.45.1464P 10.1063/1.1727786
- D. Poland H.A. Scheraga 1966 J. Chem. Phys. 45 1464 1966JChPh..45.1464P 10.1063/1.1727786
- (1966) J. Chem. Phys. , vol.45 , pp. 1464
- Poland, D.¹ Scheraga, H.A.²

44
- 10844229039
- Generalized Poland-Scheraga model for DNA hybridization
- DOI 10.1002/bip.20140
- T. Garel H. Orland 2004 Biopolymers 75 453 10.1002/bip.20140 (Pubitemid 39664658)
- (2004) Biopolymers , vol.75 , Issue.6 , pp. 453-467
- Garel, T.¹ Orland, H.²

45
- 0032539693
- A unified view of polymer, dumbbell, and oligonucleotide DNA nearest- neighbor thermodynamics
- DOI 10.1073/pnas.95.4.1460
- J. SantaLucia jr. 1998 Proc. Natl. Acad. Sci. U.S.A. 95 1460 1998PNAS...95.1460S 10.1073/pnas.95.4.1460 (Pubitemid 28103414)
- (1998) Proceedings of the National Academy of Sciences of the United States of America , vol.95 , Issue.4 , pp. 1460-1465
- Santalucia Jr., J.¹

46
- 0043123153
- Vienna RNA secondary structure server
- DOI 10.1093/nar/gkg599
- I.L. Hofacker 2003 Nucleic Acids Res. 31 3429 10.1093/nar/gkg599 (Pubitemid 37442172)
- (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3429-3431
- Hofacker, I.L.¹

47
- 23144440350
- DINAMelt web server for nucleic acid melting prediction
- DOI 10.1093/nar/gki591
- N.R. Markham M. Zuker 2005 Nucleic Acids Res. 33 W577 10.1093/nar/gki591 (Pubitemid 44529988)
- (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
- Markham, N.R.¹ Zuker, M.²

48
- 33744995763
- Prediction of RNA secondary structures: From theory to models and real molecules
- DOI 10.1088/0034-4885/69/5/R04, PII S0034488506367644, R04
- P. Schuster 2006 Rep. Prog. Phys. 69 1419 2228482 2006RPPh...69.1419S 10.1088/0034-4885/69/5/R04 (Pubitemid 43862450)
- (2006) Reports on Progress in Physics , vol.69 , Issue.5 , pp. 1419-1477
- Schuster, P.¹

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.