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Thermodynamic properties of a DNA hairpin under a pulling force

  • Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei 230026, China

Funds:  Supported by the China Postdoctoral Science Foundation (2015M581998), the Fundamental Research Funds for the Central Universities of China (WK2060200020).
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https://doi.org/10.3969/j.issn.0253-2778.2017.12.004
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  • Author Bio:

    ZHANG Donghua, female, born in 1991, Master. Research field: soft matter physics and biological physics. E-mail: zdh2014@mail.ustc.edu.cn

  • Corresponding author: YU Wancheng
  • Received Date: 30 March 2017
  • Rev Recd Date: 02 June 2017
  • Publish Date: 30 December 2017
    Abstract

  • Abstract

    The phase transition of a DNA hairpin under a pulling force was investigated by using the two-dimensional (2D) Langevin dynamics simulations. It is found that the unfolded probability could be quantitatively expressed as a function of the pulling force, which is interpreted from the perspective of statistical mechanics. Then, by performing vast simulations with different parameter sets, the force-intensity of base pairing and the force-temperature phase diagram was plotted, respectively. It is shown that the increasing intensity of base pairing and the decreasing temperature are in favor of the folded states. The phase diagrams obtained in the present work are conductive to deepening understanding of the thermodynamic properties of a DNA hairpin under a pulling force.

    Abstract

    The phase transition of a DNA hairpin under a pulling force was investigated by using the two-dimensional (2D) Langevin dynamics simulations. It is found that the unfolded probability could be quantitatively expressed as a function of the pulling force, which is interpreted from the perspective of statistical mechanics. Then, by performing vast simulations with different parameter sets, the force-intensity of base pairing and the force-temperature phase diagram was plotted, respectively. It is shown that the increasing intensity of base pairing and the decreasing temperature are in favor of the folded states. The phase diagrams obtained in the present work are conductive to deepening understanding of the thermodynamic properties of a DNA hairpin under a pulling force.
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    • References(31)
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    ERRAMI J, PEYRARD M, THEODORAKOPOULOS N. Modeling DNA beacons at the mesoscopic scale [J]. The European Physical Journal E，2007, 23: 397-411.
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    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.
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    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.
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    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.
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    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.
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    [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.
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    [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.
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