SELECTED PUBLICATIONS

  1. J Chen, Q Tang, S Guo, C Lu, S Le, J Yan(2017) "Parallel triplex structure formed between stretched single-stranded DNA and homologous duplex DNA. " Nucleic Acids Research, 45(17), 10032-10041.https://doi.org/10.1093/nar/gkx628
  2. S Le, E Serrano, R Kawamura, B Carrasco, J Yan, JC Alonso(2017)"Bacillus subtilis RecA with DprA–SsbA antagonizes RecX function during natural transformation" Nucleic Acids Research, 45(15), 8873-8885. https://doi.org/10.1093/nar/gkx583
  3. X Zhao, X Zeng, C Lu, J Yan(2017)"Studying the mechanical responses of proteins using magnetic tweezers" Nanotechnology, 28(41), 8873-8885. http://iopscience.iop.org/article/10.1088/1361-6528/aa837e/meta
  4. G Yuan, S Le, M Yao, H Qian, X Zhou, J Yan, H Chen(2017) "Elasticity of the Transition State Leading to an Unexpected Mechanical Stabilization of Titin Immunoglobulin Domains" Angewandte Chemie, 129(20), 5582-5585. https://doi.org/10.1002/ange.201700411
  5. AK Efremov, RS Winardhi, J Yan(2017) "Theoretical Methods for Studying DNA Structural Transitions under Applied Mechanical Constraints" Polymers, 9(2), 74. https://doi.org/10.3390/polym9020074
  6. You, H., Lattmann, S., Rhodes, D., and Yan, J. (2017). "RHAU helicase stabilizes G4 in its nucleotide-free state and destabilizes G4 upon ATP hydrolysis." Nucleic Acids Research, 46(1), 206-214. https://doi.org/10.1093/nar/gkw881
  7. Winardhi, R. S., Tang, Q., Chen, J., Yao, M., and Yan, J. (2016). " Probing Small Molecule Binding to Unfolded Polyprotein Based on its Elasticity and Refolding." Biophysical Journal, 111(11), 2349-2357. http://dx.doi.org/10.1016/j.bpj.2016.10.031
  8. Li, W., Chen, P., Yu, J., Dong, L., Liang, D., Feng, J., ... and Li, M. (2016). " FACT Remodels the Tetranucleosomal Unit of Chromatin Fibers for Gene Transcription." Molecular Cell, 64(1), 120-133.http://dx.doi.org/10.1016/j.molcel.2016.08.024
  9. Kulemzina, I., Ang, K., Zhao, X., Teh, J. T., Verma, V., Suranthran, S., ... and Yan, J. (2016). " A Reversible Association between Smc Coiled Coils Is Regulated by Lysine Acetylation and Is Required for Cohesin Association with the DNA." Molecular Cell, 63(6),1044-1054. http://dx.doi.org/10.1016/j.molcel.2016.08.008
  10. Efremov, A. K., Winardhi, R. S., and Yan, J. (2016). " Transfer-matrix calculations of DNA polymer micromechanics under tension and torque constraints." Physical Review E,94(3),032404.https://doi.org/10.1103/PhysRevE.94.032404
  11. Yan, J. (2016)." Mechanisms of DNA disentangling by type II topoisomerases. Comment on" Disentangling DNA molecules" by Alexander Vologodskii." Physics of Life Reviews,18,158-159.. 10.1016/j.plrev.2016.09.005
  12. Yao, M., Goult, B. T., Klapholz, B., Hu, X., Toseland, C.P., Guo, Y., Cong, P., Sheetz, M. P., and Yan, J. (2016). "The mechanical response of talin." Nature Communications, 7: 11966. [DOI: 10.1038/ncomms11966]
  13. Cong, P.W. and Yan, J. (2016). "Recent progress on the mechanics of sharply bent DNA." Sci. China Phys. Mech. Astron., 59: 680001. [DOI: 10.1007/s11433-016-0099-0]
  14. Yang, Z., Yuan, G., Zhai, W., Yan, J. and Chen, H. (2016). "The kinetics of force-dependent hybridization and strand-peeling of short DNA fragments." Sci. China Phys. Mech. Astron., 59: 680013. [DOI: 10.1007/s11433-016-0112-0]
  15. Desai, S.K., Winardhi, R.S., Periasamy, S., Dykas, M.M., Yan, J. and Kenney, L.J. (2016). "The horizontally-acquired response regulator SsrB drives a Salmonella lifestyle switch by relieving biofilm silencing." eLife, 5: e10747. [DOI: 10.7554/eLife.10747]
  16. Le, S., Liu, R., Lim, C. T., Yan, J. (2016). "Uncovering mechanosensing mechanisms at the single protein level using magnetic tweezers." Methods, 94: 13-18. [DOI: 10.1016/j.ymeth.2015.08.020]
  17. Cong, P., Dai, L., Chen, H., van der Maarel, J.R.C., Doyle, P.S., and Yan, J. (2015). "Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA." Biophysical Journal, 109: 2338-2351. [DOI: 10.1016/j.bpj.2015.10.016]
  18. Lee, S.Y., Lim, C.J., Dröge, P., Yan, J. (2015). "Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF." Scientific Reports, 5: 18146. [DOI: 10.1038/srep18146]
  19. You, H., Wu, J., Shao, F., Yan, J. (2015). "Stability and Kinetics of c-MYC Promoter G-Quadruplexes Studied by Single-Molecule Manipulation." Journal of the American Chemical Society (Communication), 137: 2424-2427. [DOI: 10.1021/ja511680u]
  20. Li, W., Wong, W.J., Lim, C.J., Ju, H.P., Li, M. Yan, J., Wang, P.Y. (2015). "Complex kinetics of DNA condensation revealed through DNA twist tracing." Physical Review E, 92: 022707. [DOI: 10.1103/PhysRevE.92.022707]
  21. Winardhi, R.S., Yan, J., Kenney, L. J. (2015). "H-NS Regulates Gene Expression and Compacts the Nucleoid: Insights from Single-Molecule Experiments." Biophysical Journal, 109: 1321-1329. [DOI: 10.1016/j.bpj.2015.08.016]
  22. Le, S., Yao, M., Chen, J., Efremov, A. K., Azimi, S., and Yan, J. (2015). "Disturbance-free rapid solution exchange for magnetic tweezers single-molecule studies." Nucleic acids research, 43: e113. [DOI: 10.1093/nar/gkv554]
  23. Efremov, A. K., Qu, Y., Maruyama, H., Lim, C. J., Takeyasu, K., Yan, J. (2015). "Transcriptional repressor TrmBL2 from Thermococcus kodakarensis forms filamentous nucleoprotein structures and competes with histones for DNA binding in a salt- and DNA supercoiling-dependent manner." J. Biol. Chem., 290: 15770-15784. [DOI: 10.1074/jbc.M114.626705jbc.M114.626705]
  24. Ladoux, B., Nelson, W. J., Yan, J., and Mège, R.M. (2015). "The minimal mechanosensing machinery at work at cell-cell contacts." Integrative Biology, 7: 1109-1119. [DOI: 10.1039/C5IB00070J]
  25. Yao, M., Chen, H., Yan, J. (2015). "Thermodynamics of force-dependent folding and unfolding of small protein and nucleic acid structures." Integrative Biology, 7: 1154-1160. [DOI: 10.1039/C5IB00038F]
  26. Chen, J., Le, S., Basu, A., Chazin, W. J., and Yan, J. (2015). "Mechanochemical regulations of RPA's binding to ssDNA." Scientific Reports., 5: 9296. [DOI: 10.1038/srep09296]
  27. Chen, H., Yuan, G., Winardhi, R.S., Yao, M., Popa, I., Fernandez, J.M., Yan, J. (2015). "Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces." Journal of the American Chemical Society, 137: 3540-3546. [DOI: 10.1021/ja5119368]
  28. You, H., Wu, J., Shao, F., Yan, J. (2015). "Stability and Kinetics of c-MYC Promoter G-Quadruplexes Studied by Single-Molecule Manipulation." Journal of the American Chemical Society (Communication), 137: 2424-2427. [DOI: 10.1021/ja511680u]
  29. Yan, J., Yao, M., Goult, B.T., Sheetz, M.P. (2014). "Talin Dependent Mechanosensitivity of Cell Focal Adhesions." Cellular and Molecular Bioengineering, 8: 151-159. [DOI: 10.1007/s12195-014-0364-5]
  30. Winardhi, R.S., Castang, S., Dove, S.L., Yan, J. (2014). "Single-Molecule Study on Histone-Like Nucleoid- Structuring Protein (H-NS) Paralogue in Pseudomonas aeruginosa: MvaU Bears DNA Organization Mode Similarities to MvaT." PLoS One, 9: e112246. [DOI: 10.1371/journal.pone.0112246]
  31. Zhang, X., Qu, Y., Chen, H., Rouzina, I., Zhang, S., Doyle, P., Yan, J. (2014). "Interconversion between three overstretched DNA structures." Journal of the American Chemical Society, 136: 16073 -16080. [DOI: 10.1021/ja5090805]
  32. Kundukad,B., Yan, J., Doyle, P.S. (2014). "Effect of YOYO-1 on the mechanical properties of DNA." Soft Matter, 10: 9721-9728. [DOI: 10.1039/C4SM02025A]
  33. Le, S., Chen, H, Zhang, X., Chen, J., Patil, K., Muniyappa, K. and Yan, J. (2014). "Mechanical force antagonizes the inhibitory effects of RecX on RecA filament formation in Mycobacterium tuberculosis." Nucleic Acids Research, 42: 11992-11999. [DOI: 10.1093/nar/gku899]
  34. Yao, M., Qiu, W., Liu, R. , Efremov, A.K., Cong, P., Seddiki, R., Payre, M., Lim, C.T., Ladoux, B., Me`ge, R.M., and Yan, J. (2014). "Force-dependent conformational switch of alpha-catenin controls vinculin binding." Nature Communications, 5:4525. [DOI: 10.1038/ncomms5525]
  35. Lim, C.J., Kenney, L.J., and Yan, J. (2014). "Single-molecule studies on the mechanical interplay between DNA supercoiling and H-NS DNA architectural properties." Nucleic Acids Research, 42: 8369-8378. [DOI: 10.1093/nar/gku566]
  36. You, H., Zeng, X., Xu, Y., Lim, C.,Efremov, A.K., Phan, A.T., and Yan, J. (2014). "Dynamics and stability of polymorphic human telomeric G-quadruplex under tension." Nucleic Acids Research, 42:8789-8795. [DOI: 10.1093/nar/gku581]
  37. Xu, Y., Chen, H., Qu, Y., Efremovb, A.K., Li, M., Ou-Yang, Z.C., Liu, D., and Yan, J. (2014). "Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif." Chin. Phys. B, 23:068702. [DOI: 10.1088/1674-1056/23/6/068702]
  38. Yao, M., Goult, B.T., Chen, H., Cong, P., Sheetz, M.P., and Yan, J. (2014). "Mechanical activation of vinculin binding to talin locks talin in an unfolded conformation." Scientific Reports, 4:4610. [DOI: 10.1038/srep04610]
  39. Winardhi, R.S., Gulvady R., Mellies J. L., and Yan, J (2014). "Locus of Enterocyte Effacement-Encoded Regulator (Ler) of pathogenic Escherichia coli Competes Off Nucleoid Structuring Protein H-NS through Non-Cooperative DNA Binding." J. Biol. Chem., 89:13739-13750. [DOI: 10.1074/jbc.M113.545954]
  40. Le, S., Chen, H., Cong, P., Lin, J., Dröge, P., and Yan, J. "Mechanosensing of DNA bending in a single specific protein-DNA complex." Scientific Reports, 3: 3508.[DOI: 10.1038/srep03508]
  41. Fu, H.X., Le, S.M., Muniyappa, K., and Yan, J. (2013). "Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA." PLoS ONE. 8(11): e66712.[DOI: 10.1371/journal.pone.0066712]
  42. Chen, H., Chandrasekar, S., Sheetz, M. P., Stossel, T. P., Nakamura, F., and Yan, J. (2013). "Mechanical perturbation of filamin A immunoglobulin repeats 20-21 reveals potential non-equilibrium mechanochemical partner binding function." Scientific Reports. 3:1642. [DOI: 10.1038/srep01642]
  43. Qu, Y., Lim, C.J., Whang, Y.R., Liu,J., and Yan, J. (2013). "Mechanism of DNA Organization by Mycobacterium tuberculosis Protein Lsr2." Nucleic Acids Research. 41(10):5263-5272. [DOI: 10.1093/nar/gkt249]
  44. Zhang, X., Chen, H., Le, S., Rouzina, I., Doyle, P.S., and Yan, J. (2013). "Revealing the Competition between Peeled-ssDNA, Melting Bubbles and S-DNA during DNA Overstretching by Single-Molecule Calorimetry." Proceedings of the National Academy of Sciences. 110:3859-3864.[DOI: 10.1073/pnas.1213740110]
  45. Fu, H.X., Le, S.M., Chen, H., Muniyappa, K., and Yan, J. (2013). "Force and ATP hydrolysis dependent regulation of RecA nucleoprotein filament by single-stranded DNA binding protein." Nucleic Acids Research. 41(2):924-932.[DOI: 10.1093/nar/gks1162]
  46. Lim, C.J., Lee, S.Y., Teramoto, J., Ishihama, A., and Yan, J. (2013). "The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia." Nucleic Acids Research. 41(2):746-753.[DOI: 10.1093/nar/gks1126]
  47. Khan, K., Karthikeyan, U., Li, Y., Yan, J., and Muniyappa, K. (2012). "Single-Molecule DNA Analysis Reveals That Yeast Hop1 Protein Promotes DNA Folding and Synapsis:Implications for Condensation of Meiotic Chromosomes." ACS Nano. 6(12):10658-10666.[DOI: 10.1021/nn3038258]
  48. Lin, J., Chen, H., Droge, P., and Yan, J. (2012). "Physical organization of DNA by multiple non-specific DNA-binding modes of Integration Host Factor (IHF)." PLoS ONE. 7(11): e49885.[DOI: 10.1371/journal.pone.0049885]
  49. Li, W., Wang, P.Y., Yan, J., and Li, M. (2012). "Impact of DNA twist accumulation on progressive helical wrapping of torsionally constrained DNA." Physical Review Letters 109(21): 218102. [DOI: 10.1103/PhysRevLett.109.218102]
  50. Lim, C.J., Lee, S.Y., Kenney, L.J., and Yan J. (2012). "Nucleoprotein filament formation is the structural basis for H-NS gene silencing." Scientific Reports. 2:509. [DOI: 10.1038/srep00509]
  51. Winardhi, R.S., Fu, W., Castang, S., Li, Y., Dove, S.L. and Yan J. (2012). "Higher order oligomerization is required for H-NS family member MvaT to form gene-silencing nucleoprotein filaments." Nucleic Acids Research. 40:8942-8952. [DOI: 110.1093/nar/gks669] This work was recommended at Faculty of 1000: LINK
  52. Zhang X, Chen H, Fu H, Doyle PS, Yan J (2012). "Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements." Proceedings of the National Academy of Sciences. 109:8103-8108. [DOI: 10.1073/pnas.1109824109] This work was highlighted in a recent issue (Volume 97, Issue 8) of Biopolymers: LINK News Highlight: Science Daily : Phys Org : Physics News
  53. Lim, C.J., Y.R. Whang, L.J. Kenney and J. Yan (2012). "Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility." Nucleic Acids Research 40:3316-3328. [DOI: 10.1093/nar/gkr1247]
  54. Chen, H, X.Y. Zhu, P.W. Cong, M.P. Sheetz, F. Nakamura, and J. Yan (2011). "Differential Mechanical Stability of Filamin A Rod Segments." Biophysical Journal 101:1231-1237. [DOI: 10.1016/j.bpj.2011.07.028]
  55. Fu, H.X., B.S. Freedman, C.T. Lim, R. Heald, and J. Yan (2011). "Atomic Force Microscope Imaging of Chromatin Assembled in Xenopus laevis Egg Extract." Chromosoma 120:245-254. [DOI: 10.1007/s00412-010-0307-4]
  56. Chen, H, H.X. Fu, X.Y. Zhu, P.W. Cong, F. Nakamura, and J. Yan (2011). "Improved High Force Magnetic Tweezers for Stretching and Refolding of Proteins and Short DNA." Biophysical Journal 100: 517-523. [DOI: 10.1007/s00412-010-0307-4]
  57. Fu, H.X., H Chen, X.H. Zhang, Y QU, J.F. Marko and J. Yan (2011; first published online: Dec 21, 2010). "Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching." Nucleic Acids Research 39:3473-3481. [DOI: 10.1093/nar/gkq1278]
  58. Walthers, D., Y Li, Y Liu, S A Ganesh, J Yan and L.J. Kenney (2011). "The salmonella enterica response regulator SsrB relieves H-NS silencing by displacing H-NS bound in polymerization mode and directly activates transcription." Journal Of Biological Chemistry 286: 1895-1902. [DOI: 10.1074/jbc.M110.164962]
  59. Yan, J.(2010). "DNA binding by bacterial nucleoid proteins and the DNA overstretching transition. Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Mark C. Williams et al." Physics of Life Reviews 7:342-343. [DOI: 10.1016/j.plrev.2010.06.003]
  60. Liu, Y.J., J. Wu, H.Chen, C.L. Hew, and J. Yan (2010). "DNA Condensates Organized by the Capsid Protein VP15 in White Spot Syndrome Virus." Virology 408 :197-203. [DOI: 10.1016/j.virol.2010.09.008]
  61. Fu, H.X., H.Chen, J.F. Marko, and J. Yan (2010). "Two distinct overstretched DNA states." Nucleic Acid Research 38 :5594-5600. [DOI: 10.1093/nar/pkq309]
  62. Liu, Y.J., H.Chen, L.J. Kenney, and J. Yan (2010). "A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes." Genes & Development 24:339-344. [DOI: 10.1101/gad.1883510]
  63. Chen, H., Y.Liu, Z. Zhou, L. Hu, Z-C. Ou-Yang, and J. Yan (2009). "Temperature dependence of circular DNA topological states." Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 79(4): 041962. [DOI: 10.1103/PhysRevE.79.041926]
  64. Lubrich, D., J. Lin., and J. Yan, (2008). "A Contractile DNA Machine." Angewandte Chemie International Edition 47(37): 7026-7028. [DOI: 10.1002/anie.200800476]
  65. Chen, H. and J. Yan (2008). "Effects of kink and flexible hinge defects on mechanical responses of short double-stranded DNA molecules." Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 77(4): 041907-8. [DOI: 10.1103/PhysRevE.77.041907]
  66. Ranjith, P., J. Yan, and J.F. Marko (2007). "Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts." Proceedings of the National Academy of Sciences 104(34): 13649-13654. [DOI: 10.1073/pnas.0701459104]
  67. Bao, Q., H. Chen, Y.J. Liu, J. Yan, P. Dröge, and C.A. Davey (2007). "A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending." Journal of Molecular Biology 367(3): 731-740. [DOI: 10.1016/j.jmb.2006.09.082]
  68. Yan, J., T. J. Maresca, et al. (2007). "Micromanipulation Studies of Chromatin Fibers in Xenopus Egg Extracts Reveal ATP-dependent Chromatin Assembly Dynamics." Molecular Biology of the Cell 18(2): 464-474. [DOI: 10.1091/mbc.E06-09-0800]
  69. Fu, W. B., X. L. Wang, X.H. Zhang, S.Y. Ran, J. Yan, and M. Li (2006). "Compaction Dynamics of Single DNA Molecules under Tension." Journal of the American Chemical Society 128(47): 15040-15041. [DOI: 10.1021/ja064305a]
  70. Skoko, D., J. Yan, RC Johnson, and J.F. Marko (2005). "Low-Force DNA Condensation and Discontinuous High-Force Decondensation Reveal a Loop-Stabilizing Function of the Protein Fis." Physical Review Letters 95(20): 208101-4. [DOI: 10.1103/PhysRevLett.95.208101]
  71. Yan, J., R. Kawamura, and J.F. Marko (2005). "Statistics of loop formation along double helix DNAs." Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 71(6): 061905-17. [DOI: 10.1103/PhysRevE.71.061905]
  72. Yan, J. and J. F. Marko (2004). "Localized Single-Stranded Bubble Mechanism for Cyclization of Short Double Helix DNA." Physical Review Letters 93(10): 108108. [DOI: 10.1103/PhysRevLett.93.108108]
  73. Yan, J., D. Skoko, and J. F. Marko (2004). "Near-field-magnetic-tweezer manipulation of single DNA molecules." Physical Review E 70(1): 011905. [DOI: 10.1103/PhysRevE.70.011905]
  74. Yan, J. and J. F. Marko (2003). "Effects of DNA-distorting proteins on DNA elastic response." Physical Review E 68(1): 011905. [DOI: 10.1103/PhysRevE.68.011905]
  75. Yan, J., M. O. Magnasco, and J.F. Marko (1999). "A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases." Nature 401(6756): 932-935. [DOI: 10.1038/44872]