Journal articles: 'DNA unzipping'

1

Krautbauer, Rupert, Matthias Rief, and Hermann E. Gaub. "Unzipping DNA Oligomers." Nano Letters 3, no. 4 (April 2003): 493–96. http://dx.doi.org/10.1021/nl034049p.

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2

Chakrabarti, Buddhapriya, and David R. Nelson. "Shear Unzipping of DNA†." Journal of Physical Chemistry B 113, no. 12 (March 26, 2009): 3831–36. http://dx.doi.org/10.1021/jp808232p.

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3

Kafri, Y., D. Mukamel, and L. Peliti. "Melting and unzipping of DNA." European Physical Journal B - Condensed Matter 27, no. 1 (May 1, 2002): 135–46. http://dx.doi.org/10.1140/epjb/e20020138.

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4

Amnuanpol, Sitichoke. "Physical origin of DNA unzipping." Journal of Biological Physics 42, no. 1 (August 26, 2015): 69–82. http://dx.doi.org/10.1007/s10867-015-9393-0.

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5

Lubensky, David K., and David R. Nelson. "Pulling Pinned Polymers and Unzipping DNA." Physical Review Letters 85, no. 7 (August 14, 2000): 1572–75. http://dx.doi.org/10.1103/physrevlett.85.1572.

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6

Volkov, S. N., and A. V. Solov’yov. "The mechanism of DNA mechanical unzipping." European Physical Journal D 54, no. 3 (June 30, 2009): 657–66. http://dx.doi.org/10.1140/epjd/e2009-00194-5.

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7

CALVO, J., J. NIETO, J. SOLER, and M. O. VÁSQUEZ. "ON A DISPERSIVE MODEL FOR THE UNZIPPING OF DOUBLE-STRANDED DNA MOLECULES." Mathematical Models and Methods in Applied Sciences 24, no. 03 (December 29, 2013): 495–511. http://dx.doi.org/10.1142/s0218202513500577.

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The paper deals with the analysis of a nonlinear Fokker–Planck equation modeling the mechanical unzipping of double-stranded DNA under the influence of an applied force. The dependent variable is the probability density of unzipping m base pairs. The nonlinear Fokker–Planck equation we propose here is obtained when we couple the model proposed in [D. K. Lubensky and D. R. Nelson, Pulling pinned polymers and unzipping DNA, Phys. Rev. Lett.85 (2000) 1572–1575] with a transcendental equation for the applied force. The resulting model incorporates nonlinear effects in a different way than the usual models in kinetic theory. We show the well-posedness of this model. For that we require a combination of techniques coming from second-order kinetic equations and compensated compactness arguments in conservation laws.

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8

Mathé, Jérôme, Hasina Visram, Virgile Viasnoff, Yitzhak Rabin, and Amit Meller. "Nanopore Unzipping of Individual DNA Hairpin Molecules." Biophysical Journal 87, no. 5 (November 2004): 3205–12. http://dx.doi.org/10.1529/biophysj.104.047274.

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9

Viasnoff, V., N. Chiaruttini, J. Muzard, and U. Bockelmann. "Force fluctuations assist nanopore unzipping of DNA." Journal of Physics: Condensed Matter 22, no. 45 (October 29, 2010): 454122. http://dx.doi.org/10.1088/0953-8984/22/45/454122.

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10

Li, Xinqiong, Guiqin Song, Linqin Dou, Shixin Yan, Ming Zhang, Weidan Yuan, Shirong Lai, et al. "The structure and unzipping behavior of dumbbell and hairpin DNA revealed by real-time nanopore sensing." Nanoscale 13, no. 27 (2021): 11827–35. http://dx.doi.org/10.1039/d0nr08729g.

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11

Lin, Yao, Xin Shi, Shao-Chuang Liu, Yi-Lun Ying, Qiao Li, Rui Gao, Farkhondeh Fathi, Yi-Tao Long, and He Tian. "Characterization of DNA duplex unzipping through a sub-2 nm solid-state nanopore." Chemical Communications 53, no. 25 (2017): 3539–42. http://dx.doi.org/10.1039/c7cc00060j.

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12

Weeks, J. D., J. B. Lucks, Y. Kafri, C. Danilowicz, D. R. Nelson, and M. Prentiss. "Pause Point Spectra in DNA Constant-Force Unzipping." Biophysical Journal 88, no. 4 (April 2005): 2752–65. http://dx.doi.org/10.1529/biophysj.104.047340.

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13

Hiroshima, M., and M. Tokunaga. "DNA Unzipping measurement with an ultrasensitive probe microscope." Seibutsu Butsuri 43, supplement (2003): S223. http://dx.doi.org/10.2142/biophys.43.s223_2.

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14

Lakatos, Greg, Tom Chou, Birger Bergersen, and Gren N. Patey. "First passage times of driven DNA hairpin unzipping." Physical Biology 2, no. 3 (September 12, 2005): 166–74. http://dx.doi.org/10.1088/1478-3975/2/3/004.

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15

Bergues-Pupo, Ana Elisa, Fernando Falo, and Alessandro Fiasconaro. "Resonant optimization in the mechanical unzipping of DNA." EPL (Europhysics Letters) 105, no. 6 (March 1, 2014): 68005. http://dx.doi.org/10.1209/0295-5075/105/68005.

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16

Singh, N., and Y. Singh. "Statistical theory of force-induced unzipping of DNA." European Physical Journal E 17, no. 1 (March 18, 2005): 7–19. http://dx.doi.org/10.1140/epje/i2004-10100-7.

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17

Stachiewicz, Anna, and Andrzej Molski. "Diffusive dynamics of DNA unzipping in a nanopore." Journal of Computational Chemistry 37, no. 5 (October 31, 2015): 467–76. http://dx.doi.org/10.1002/jcc.24236.

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18

Koch, Steven J., Alla Shundrovsky, Benjamin C. Jantzen, and Michelle D. Wang. "Probing Protein-DNA Interactions by Unzipping a Single DNA Double Helix." Biophysical Journal 83, no. 2 (August 2002): 1098–105. http://dx.doi.org/10.1016/s0006-3495(02)75233-8.

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19

Tee, Shern Ren, and Zhisong Wang. "How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures." ACS Omega 3, no. 1 (January 10, 2018): 292–301. http://dx.doi.org/10.1021/acsomega.7b01692.

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20

Meng, Fu-Na, Zi-Yuan Li, Yi-Lun Ying, Shao-Chuang Liu, Junji Zhang, and Yi-Tao Long. "Structural stability of the photo-responsive DNA duplexes containing one azobenzene via a confined pore." Chemical Communications 53, no. 68 (2017): 9462–65. http://dx.doi.org/10.1039/c7cc04599a.

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Herein, the structural stability of single azobenzene modified DNA duplexes, including the trans form and cis form, has been examined separately based on their distinguishable unzipping kinetics from the mixture by an α-hemolysin nanopore.

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21

Bockelmann, U., and V. Viasnoff. "Theoretical Study of Sequence-Dependent Nanopore Unzipping of DNA." Biophysical Journal 94, no. 7 (April 2008): 2716–24. http://dx.doi.org/10.1529/biophysj.107.111732.

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22

OHARA, Masayuki, Yusuke SEKIYA, and Ryuji KAWANO. "Hairpin DNA Unzipping Analysis Using a Biological Nanopore Array." Electrochemistry 84, no. 5 (2016): 338–41. http://dx.doi.org/10.5796/electrochemistry.84.338.

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23

Bhattacharjee, Somendra M., and D. Marenduzzo. "DNA sequence from the unzipping force? One mutation problem." Journal of Physics A: Mathematical and General 35, no. 26 (June 21, 2002): L349—L356. http://dx.doi.org/10.1088/0305-4470/35/26/101.

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24

Xiao-Feng, Wang, Lei Xiao-Ling, and Fang Hai-Ping. "What Governs the Unzipping Process of Double-Stranded DNA." Chinese Physics Letters 23, no. 5 (April 28, 2006): 1339–42. http://dx.doi.org/10.1088/0256-307x/23/5/076.

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25

Kapri, Rajeev, and Somendra M. Bhattacharjee. "Unzipping DNA by force: thermodynamics and finite size behaviour." Journal of Physics: Condensed Matter 18, no. 14 (March 24, 2006): S215—S223. http://dx.doi.org/10.1088/0953-8984/18/14/s06.

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26

Kumar, Sanjay, and Debaprasad Giri. "Probability distribution analysis of force induced unzipping of DNA." Journal of Chemical Physics 125, no. 4 (July 28, 2006): 044905. http://dx.doi.org/10.1063/1.2219115.

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27

Bergues-Pupo, A. E., J. M. Bergues, and F. Falo. "Unzipping of DNA under the influence of external fields." Physica A: Statistical Mechanics and its Applications 396 (February 2014): 99–107. http://dx.doi.org/10.1016/j.physa.2013.10.050.

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28

Mathé, J., A. Arinstein, Y. Rabin, and A. Meller. "Equilibrium and irreversible unzipping of DNA in a nanopore." Europhysics Letters (EPL) 73, no. 1 (January 2006): 128–34. http://dx.doi.org/10.1209/epl/i2005-10368-7.

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29

Volkov, Sergey N., Ekaterina V. Paramonova, Alexander V. Yakubovich, and Andrey V. Solov’yov. "Micromechanics of base pair unzipping in the DNA duplex." Journal of Physics: Condensed Matter 24, no. 3 (December 16, 2011): 035104. http://dx.doi.org/10.1088/0953-8984/24/3/035104.

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30

Cervantes-Salguero, Keitel, Ibuki Kawamata, Shin-ichiro M. Nomura, and Satoshi Murata. "Unzipping and shearing DNA with electrophoresed nanoparticles in hydrogels." Physical Chemistry Chemical Physics 19, no. 21 (2017): 13414–18. http://dx.doi.org/10.1039/c7cp02214j.

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31

Lam, Pui-Man, J. C. S. Levy, and Hanchen Huang. "Excluded volume effect in unzipping DNA with a force." Biopolymers 73, no. 3 (2004): 293–300. http://dx.doi.org/10.1002/bip.10584.

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32

Herskowitz, Lawrence J., Anthony L. Salvagno, Linh Le, and Steven J. Koch. "Proof of Principle for Shotgun DNA Mapping by Unzipping." Biophysical Journal 96, no. 3 (February 2009): 291a. http://dx.doi.org/10.1016/j.bpj.2008.12.1442.

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33

Dame, Remus T., Michael A. Hall, and Michelle D. Wang. "Single-Molecule Unzipping Force Analysis of HU-DNA Complexes." ChemBioChem 14, no. 15 (September 2, 2013): 1954–57. http://dx.doi.org/10.1002/cbic.201300413.

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34

Rissone, Paolo, and Felix Ritort. "Nucleic Acid Thermodynamics Derived from Mechanical Unzipping Experiments." Life 12, no. 7 (July 20, 2022): 1089. http://dx.doi.org/10.3390/life12071089.

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Force-spectroscopy techniques have led to significant progress in studying the physicochemical properties of biomolecules that are not accessible in bulk assays. The application of piconewton forces with laser optical tweezers to single nucleic acids has permitted the characterization of molecular thermodynamics and kinetics with unprecedented accuracy. Some examples are the hybridization reaction between complementary strands in DNA and the folding of secondary, tertiary, and other heterogeneous structures, such as intermediate and misfolded states in RNA. Here we review the results obtained in our lab on deriving the nearest-neighbor free energy parameters in DNA and RNA duplexes from mechanical unzipping experiments. Remarkable nonequilibrium effects are also observed, such as the large irreversibility of RNA unzipping and the formation of non-specific secondary structures in single-stranded DNA. These features originate from forming stem-loop structures along the single strands of the nucleic acid. The recently introduced barrier energy landscape model quantifies kinetic trapping effects due to stem-loops being applicable to both RNA and DNA. The barrier energy landscape model contains the essential features to explain the many behaviors observed in heterogeneous nucleic-acid folding.

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35

Bujold, Katherine E., Johans Fakhoury, Thomas G. W. Edwardson, Karina M. M. Carneiro, Joel Neves Briard, Antoine G. Godin, Lilian Amrein, et al. "Sequence-responsive unzipping DNA cubes with tunable cellular uptake profiles." Chem. Sci. 5, no. 6 (2014): 2449–55. http://dx.doi.org/10.1039/c4sc00646a.

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36

Barbieri, Carlo, Simona Cocco, Rémi Monasson, and Francesco Zamponi. "Dynamical modeling of molecular constructions and setups for DNA unzipping." Physical Biology 6, no. 2 (July 1, 2009): 025003. http://dx.doi.org/10.1088/1478-3975/6/2/025003.

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37

Liu, Aihua, Qitao Zhao, D. M. Milan Krishantha, and Xiyun Guan. "Unzipping of Double-Stranded DNA in Engineered α-Hemolysin Pores." Journal of Physical Chemistry Letters 2, no. 12 (May 23, 2011): 1372–76. http://dx.doi.org/10.1021/jz200525v.

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38

Lam, Pui-Man, and Yi Zhen. "Force induced unzipping of DNA with long range correlated noise." Journal of Statistical Mechanics: Theory and Experiment 2011, no. 06 (June 30, 2011): P06023. http://dx.doi.org/10.1088/1742-5468/2011/06/p06023.

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39

Zhang, Jie, Yunqi Yan, Soumyadyuti Samai, and David S. Ginger. "Dynamic Melting Properties of Photoswitch-Modified DNA: Shearing versus Unzipping." Journal of Physical Chemistry B 120, no. 41 (October 7, 2016): 10706–13. http://dx.doi.org/10.1021/acs.jpcb.6b08297.

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40

Kafri, Y., D. Mukamel, and L. Peliti. "Denaturation and unzipping of DNA: statistical mechanics of interacting loops." Physica A: Statistical Mechanics and its Applications 306 (April 2002): 39–50. http://dx.doi.org/10.1016/s0378-4371(02)00483-1.

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41

Muzard, J., M. Martinho, J. Mathé, U. Bockelmann, and V. Viasnoff. "DNA Translocation and Unzipping through a Nanopore: Some Geometrical Effects." Biophysical Journal 98, no. 10 (May 2010): 2170–78. http://dx.doi.org/10.1016/j.bpj.2010.01.041.

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42

Stachiewicz, Anna, and Andrzej Molski. "Sequence-Dependent Unzipping Dynamics of DNA Hairpins in a Nanopore." Journal of Physical Chemistry B 123, no. 15 (March 28, 2019): 3199–209. http://dx.doi.org/10.1021/acs.jpcb.9b00183.

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43

Lam, Pui-Man, and J. C. Levy. "Unzipping DNA from the condensed globule state—Effects of unraveling." Biopolymers 79, no. 6 (2005): 287–91. http://dx.doi.org/10.1002/bip.20292.

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44

Cocco, S., R. Monasson, and J. F. Marko. "Force and kinetic barriers to unzipping of the DNA double helix." Proceedings of the National Academy of Sciences 98, no. 15 (July 10, 2001): 8608–13. http://dx.doi.org/10.1073/pnas.151257598.

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45

Lee, C. H., C. Danilowicz, R. S. Conroy, V. W. Coljee, and M. Prentiss. "Impacts of magnesium ions on the unzipping of λ-phage DNA." Journal of Physics: Condensed Matter 18, no. 14 (March 24, 2006): S205—S213. http://dx.doi.org/10.1088/0953-8984/18/14/s05.

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46

Sutherland, Todd C., Michael J. Dinsmore, Heinz-Bernhard Kraatz, and Jeremy S. Lee. "An analysis of mismatched duplex DNA unzipping through a bacterial nanopore." Biochemistry and Cell Biology 82, no. 3 (June 1, 2004): 407–12. http://dx.doi.org/10.1139/o04-005.

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A 50-base Guide strand was synthesized that consisted of a central 10-base probe sequence flanked by two tracts of 20 adenine residues. Target sequences of 10 bases containing up to three mismatches were prepared and hybridized to the Guide strand in 1 M KCl. The transport of these constructs through single α-hemolysin pores was analysed by measuring the current blockade as a function of time. Complementary dsDNA takes significantly longer (840 ± 60 µs) to pass through the pore than a sequence of the same length containing a single (590 ± 45 µs) and a double (270 ± 50 µs) mismatch. Constructs involving three mismatches were indistinguishable from Guide ssDNA transport (120 ± 30 µs). The results suggest that dsDNA must unzip as it is transported through the nanopore. Duplexes containing mismatches unzip more quickly and can be distinguished from those with perfect complementarity.Key words: DNA unzipping, bacterial nanopores, DNA transport, single-molecule detection, DNA mismatch.

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47

Rao, V. B. "A virus DNA gate: Zipping and unzipping the packed viral genome." Proceedings of the National Academy of Sciences 106, no. 21 (May 18, 2009): 8403–4. http://dx.doi.org/10.1073/pnas.0903670106.

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48

Bockelmann, U., Ph Thomen, B. Essevaz-Roulet, V. Viasnoff, and F. Heslot. "Unzipping DNA with Optical Tweezers: High Sequence Sensitivity and Force Flips." Biophysical Journal 82, no. 3 (March 2002): 1537–53. http://dx.doi.org/10.1016/s0006-3495(02)75506-9.

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49

Nelson, David R. "Extended Abstract: Plateaus and Jumps in Single-Molecule DNA Unzipping Experiments." Journal of Biological Physics 31, no. 3-4 (December 2005): 241–42. http://dx.doi.org/10.1007/s10867-005-6062-8.

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50

Perera, Rukshan T., Aaron M. Fleming, Amberlyn M. Peterson, Jennifer M. Heemstra, Cynthia J. Burrows, and Henry S. White. "Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore." Biophysical Journal 110, no. 2 (January 2016): 306–14. http://dx.doi.org/10.1016/j.bpj.2015.11.020.

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Journal articles on the topic 'DNA unzipping'

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