Associate Professor, Department of Physics, National University of Singapore
DNA mechanics; Single molecular manipulation and imaging
Our research is based on highly sensitive single-molecule manipulation and imaging techniques. It also requires understanding mechanics of biopolymers. Our main research focuses are: Genome compaction and gene regulation in eukaryotic cells, bacteria, and viruses; Virus replication in host cells; Single-molecule detection of specific interactions between DNA and important proteins or enzymes; Micromechanics of biopolymers; Development of novel single-molecule manipulation and imaging techniques.
While being trained in theoretical physics, Dr Jie Yan built a strong interest in studying molecular cell biology using a combination of novel single-molecule biophysical methods and theoretical modeling. Since he joined the Department of Physics of NUS in 2005, he has been leading a group to study DNA-protein interactions and micromechanics of biopolymers. He became a Principal Investigator in MBI in 2009, which he will focus on studies of genome packaging in cells, gene regulation in bacteria, and mechanical responses of mechanosensing proteins to external forces.
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. Article ASAP.[DOI: 10.1021/nn3038258]
Fu, H.X., Le, S.M., Chen, H., Muniyappa, K., and Yan, J. (2012). “Force and ATP hydrolysis dependent regulation of RecA nucleoprotein filament by single-stranded DNA binding protein.” Nucleic Acids Research. Advanced Online Access.[DOI: 10.1093/nar/gks1162]
Lim, C.J., Lee, S.Y., Teramoto, J., Ishihama, A., and Yan, J. (2012). “The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia.” Nucleic Acids Research. Advanced Online Access.[DOI: 10.1093/nar/gks1126]
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]
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]
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]
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]
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]
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]
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]
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]
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]
Chen, H, H FU, X ZHU, P CONG, FN Nakamura and J Yan, “Improved Magnetic Tweezers for Stretching and Refolding of Proteins and Short DNA”. BIOPHYSICAL JOURNAL, 100, no. 2 (2011): 517-523.
Walthers, D., Y LI, Y LIU, S A Ganesh, J Yan and L.J. Kenney, “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 (2010): 1895-1902.
Yan, J, “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, no. 3 (2010): 342-343.
Chen, H, Y LIU, Jinlu WU, C L Hew and J Yan, “DNA Condensates Organized by the Capsid Protein VP15 in White Spot Syndrome Virus”. Virology, 408, no. 2 (2010): 197-203.
FU, H, H Chen, John.F Marko and J Yan, “Two Distinct Overstretched DNA States”. NUCLEIC ACIDS RESEARCH, 38, no. 16 (2010): 5594-5600.
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].
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].
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].
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].
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].
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].
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].
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].