[1] |
ZAZOPOULOS E, LALLI E, STOCCO D M, et al. DNA binding and transcriptional repression by DAX-1 blocks steroidogenesis [J]. Nature, 1997, 390: 311-315.
|
[2] |
TANG J, TEMSAMANI J, AGRAWAL S. Self-stabilized antisense oligodeoxynucleotide phosphorothioates: Properties and anti-HIV activity [J]. Nucleic Acids Research, 1993, 21: 2729-2735.
|
[3] |
FROELICH-AMMON S, GALE K C, OSHEROFF N. Site-specific cleavage of a DNA hairpin by topoisomerase II. DNA secondary structure as a determinant of enzyme recognition/cleavage [J]. The Journal of Biological Chemistry, 1994, 269: 7719-7725.
|
[4] |
TRINH T Q, SINDEN R R. The influence of primary and secondary DNA structure in deletion and duplication between direct repeats in Escherichia coli [J]. Genetics, 1993, 134: 409-422.
|
[5] |
BONNET G, KRICHEVSKY O, LIBCHABER A. Kinetics of conformational fluctuations in DNA hairpin-loops [J]. Proceedings of the National Academy of Sciences of the United States of America, 1998, 95: 8602-8606.
|
[6] |
GODDARD N L, BONNET G, KRICHEVSKY O, et al. Sequence dependent rigidity of single stranded DNA [J]. Physical Review Letters, 2000, 85: 2400-2403.
|
[7] |
WALLACE M I, YING L M, BALASUBRAMANIAN S, et al. Non-Arrhenius kinetics for the loop closure of a DNA hairpin [J]. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98: 5584-5589.
|
[8] |
ZHANG W B, CHEN S J. RNA hairpin-folding kinetics [J]. Proceedings of the National Academy of Sciences of the United States of America, 2002, 99: 1931-1936.
|
[9] |
KIM J, DOOSE S, NEUWEILER H, et al. The initial step of DNA hairpin folding: A kinetic analysis using fluorescence correlation spectroscopy [J]. Nucleic Acids Research, 2006, 34: 2516-2527.
|
[10] |
NIVON L G, SHAKHNOVICH E I. All-atom Monte Carlo simulation of GCAA RNA folding [J]. Journal of Molecular Biology, 2004, 344: 29-45.
|
[11] |
LIN M M, MEINHOLD L, SHOROKHOV D, et al. Unfolding and melting of DNA (RNA) hairpins: The concept of structure-specific 2D dynamic landscapes [J]. Physical Chemistry Chemical Physics, 2008, 10: 4227-4239.
|
[12] |
KENWARD M, DORFMAN K D. Brownian dynamics simulations of single-stranded DNA hairpins [J]. The Journal of Chemical Physics, 2009, 130: 095101.
|
[13] |
ERRAMI J, PEYRARD M, THEODORAKOPOULOS N. Modeling DNA beacons at the mesoscopic scale [J]. The European Physical Journal E,2007, 23: 397-411.
|
[14] |
SHENG Y J, HSU P H, CHEN J Z Y, et al. Loop formation of a flexible polymer with two random reactive sites [J]. Macromolecules, 2004, 37:9257-9263.
|
[15] |
SAIN A, HA B Y, TSAO H K, et al. Chain persistency in single-stranded DNA [J]. Physical Review E, 2004, 69: 061913.
|
[16] |
SHENG Y J, LIN H J, CHEN J Z Y, et al. Effect of the intermediate state on the loop-to-coil transition of a telechelic chain [J]. The Journal of Chemical Physics, 2003, 118: 8513.
|
[17] |
STEPHENSON W, KELLER S, SANTIAGO R, et al. Combining temperature and force to study folding of an RNA hairpin [J]. Physical Chemistry Chemical Physics, 2014, 16: 906-917.
|
[18] |
MEREUTA L, ASANDEI A, SEO C H, et al. Quantitative understanding of pH- and salt-mediated conformational folding of histidine-containing, β-hairpin-like peptides, through single-molecule probing with protein nanopores [J]. ACS Applied Materials & Interfaces, 2014, 6: 13242-13256.
|
[19] |
GARCIA A E, PASCHEK D. Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin [J]. Journal of the American Chemical Society, 2008, 130: 815-817.
|
[20] |
WOODSIDE M T, BEHNKE-PARKS W M, LARIZADEH T, et al. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins [J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103: 6190-6195.
|
[21] |
HANNE J, ZOCCHI G. Opening rates of DNA hairpins: Experiment and model [J]. Physical Review E, 2007, 76: 011909.
|
[22] |
MOSSA A, MANOSAS M, FORNS N, et al. Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes [J]. Journal of Statistical Mechanics: Theory and Experiment, 2009,2009:P02060.
|
[23] |
MANOSAS M, MOSSA A, FORNS N, et al. Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation [J]. Journal of Statistical Mechanics: Theory and Experiment, 2009,2009:P02061.
|
[24] |
KUMAR S, GIRI D. Probability distribution analysis of force induced unzipping of DNA [J]. The Journal of Chemical Physics, 2006, 125: 044905.
|
[25] |
MISHRA G, GIRI D, LI M S, et al. Role of loop entropy in the force induced melting of DNA hairpin [J]. The Journal of Chemical Physics, 2011, 135: 035102.
|
[26] |
BLOMMERS M, WALTERS J, HAASNOOT C, et al. Effects of base sequence on the loop folding in DNA hairpins [J]. Biochemistry, 1989, 28(18): 7491-7498.
|
[27] |
KAPRI R, BHATTACHARJEE S M, SENO F. Complete phase diagram of DNA unzipping: Eye, Y-fork and triple point [J]. Physical Review Letters, 2004, 93: 248102.
|
[28] |
MARENDUZZO D, TROVATO A, MARITAN A. Phase diagram of force-induced DNA unzipping in exactly solvable models [J]. Physical Review E, 2001, 64:031901.
|
[29] |
CHANDLER M. Introduction to Modern Statistical Mechanics [M]. New York : Oxford University Press, 1987.
|
[30] |
ERMAK D L, BUCKHOLZ H. Numerical integration of the Langevin equation: Monte Carlo simulation [J]. The Journal of Computational Physics, 1980, 35: 169-182.
|
[31] |
SHIN J, CHERSTVY A G, METZLER R. Kinetics of polymer looping with macromolecular crowding: Effects of volume fraction and crowder size [J]. Soft Matter, 2015, 11: 472-488.
|
[1] |
ZAZOPOULOS E, LALLI E, STOCCO D M, et al. DNA binding and transcriptional repression by DAX-1 blocks steroidogenesis [J]. Nature, 1997, 390: 311-315.
|
[2] |
TANG J, TEMSAMANI J, AGRAWAL S. Self-stabilized antisense oligodeoxynucleotide phosphorothioates: Properties and anti-HIV activity [J]. Nucleic Acids Research, 1993, 21: 2729-2735.
|
[3] |
FROELICH-AMMON S, GALE K C, OSHEROFF N. Site-specific cleavage of a DNA hairpin by topoisomerase II. DNA secondary structure as a determinant of enzyme recognition/cleavage [J]. The Journal of Biological Chemistry, 1994, 269: 7719-7725.
|
[4] |
TRINH T Q, SINDEN R R. The influence of primary and secondary DNA structure in deletion and duplication between direct repeats in Escherichia coli [J]. Genetics, 1993, 134: 409-422.
|
[5] |
BONNET G, KRICHEVSKY O, LIBCHABER A. Kinetics of conformational fluctuations in DNA hairpin-loops [J]. Proceedings of the National Academy of Sciences of the United States of America, 1998, 95: 8602-8606.
|
[6] |
GODDARD N L, BONNET G, KRICHEVSKY O, et al. Sequence dependent rigidity of single stranded DNA [J]. Physical Review Letters, 2000, 85: 2400-2403.
|
[7] |
WALLACE M I, YING L M, BALASUBRAMANIAN S, et al. Non-Arrhenius kinetics for the loop closure of a DNA hairpin [J]. Proceedings of the National Academy of Sciences of the United States of America, 2001, 98: 5584-5589.
|
[8] |
ZHANG W B, CHEN S J. RNA hairpin-folding kinetics [J]. Proceedings of the National Academy of Sciences of the United States of America, 2002, 99: 1931-1936.
|
[9] |
KIM J, DOOSE S, NEUWEILER H, et al. The initial step of DNA hairpin folding: A kinetic analysis using fluorescence correlation spectroscopy [J]. Nucleic Acids Research, 2006, 34: 2516-2527.
|
[10] |
NIVON L G, SHAKHNOVICH E I. All-atom Monte Carlo simulation of GCAA RNA folding [J]. Journal of Molecular Biology, 2004, 344: 29-45.
|
[11] |
LIN M M, MEINHOLD L, SHOROKHOV D, et al. Unfolding and melting of DNA (RNA) hairpins: The concept of structure-specific 2D dynamic landscapes [J]. Physical Chemistry Chemical Physics, 2008, 10: 4227-4239.
|
[12] |
KENWARD M, DORFMAN K D. Brownian dynamics simulations of single-stranded DNA hairpins [J]. The Journal of Chemical Physics, 2009, 130: 095101.
|
[13] |
ERRAMI J, PEYRARD M, THEODORAKOPOULOS N. Modeling DNA beacons at the mesoscopic scale [J]. The European Physical Journal E,2007, 23: 397-411.
|
[14] |
SHENG Y J, HSU P H, CHEN J Z Y, et al. Loop formation of a flexible polymer with two random reactive sites [J]. Macromolecules, 2004, 37:9257-9263.
|
[15] |
SAIN A, HA B Y, TSAO H K, et al. Chain persistency in single-stranded DNA [J]. Physical Review E, 2004, 69: 061913.
|
[16] |
SHENG Y J, LIN H J, CHEN J Z Y, et al. Effect of the intermediate state on the loop-to-coil transition of a telechelic chain [J]. The Journal of Chemical Physics, 2003, 118: 8513.
|
[17] |
STEPHENSON W, KELLER S, SANTIAGO R, et al. Combining temperature and force to study folding of an RNA hairpin [J]. Physical Chemistry Chemical Physics, 2014, 16: 906-917.
|
[18] |
MEREUTA L, ASANDEI A, SEO C H, et al. Quantitative understanding of pH- and salt-mediated conformational folding of histidine-containing, β-hairpin-like peptides, through single-molecule probing with protein nanopores [J]. ACS Applied Materials & Interfaces, 2014, 6: 13242-13256.
|
[19] |
GARCIA A E, PASCHEK D. Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin [J]. Journal of the American Chemical Society, 2008, 130: 815-817.
|
[20] |
WOODSIDE M T, BEHNKE-PARKS W M, LARIZADEH T, et al. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins [J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103: 6190-6195.
|
[21] |
HANNE J, ZOCCHI G. Opening rates of DNA hairpins: Experiment and model [J]. Physical Review E, 2007, 76: 011909.
|
[22] |
MOSSA A, MANOSAS M, FORNS N, et al. Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes [J]. Journal of Statistical Mechanics: Theory and Experiment, 2009,2009:P02060.
|
[23] |
MANOSAS M, MOSSA A, FORNS N, et al. Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation [J]. Journal of Statistical Mechanics: Theory and Experiment, 2009,2009:P02061.
|
[24] |
KUMAR S, GIRI D. Probability distribution analysis of force induced unzipping of DNA [J]. The Journal of Chemical Physics, 2006, 125: 044905.
|
[25] |
MISHRA G, GIRI D, LI M S, et al. Role of loop entropy in the force induced melting of DNA hairpin [J]. The Journal of Chemical Physics, 2011, 135: 035102.
|
[26] |
BLOMMERS M, WALTERS J, HAASNOOT C, et al. Effects of base sequence on the loop folding in DNA hairpins [J]. Biochemistry, 1989, 28(18): 7491-7498.
|
[27] |
KAPRI R, BHATTACHARJEE S M, SENO F. Complete phase diagram of DNA unzipping: Eye, Y-fork and triple point [J]. Physical Review Letters, 2004, 93: 248102.
|
[28] |
MARENDUZZO D, TROVATO A, MARITAN A. Phase diagram of force-induced DNA unzipping in exactly solvable models [J]. Physical Review E, 2001, 64:031901.
|
[29] |
CHANDLER M. Introduction to Modern Statistical Mechanics [M]. New York : Oxford University Press, 1987.
|
[30] |
ERMAK D L, BUCKHOLZ H. Numerical integration of the Langevin equation: Monte Carlo simulation [J]. The Journal of Computational Physics, 1980, 35: 169-182.
|
[31] |
SHIN J, CHERSTVY A G, METZLER R. Kinetics of polymer looping with macromolecular crowding: Effects of volume fraction and crowder size [J]. Soft Matter, 2015, 11: 472-488.
|