Yan Jie

 

Yan Jie

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B. Sc., Lanzou University (Physics), 1992

M.S. Lanzhou University (Physics), 1995
1st Ph.D. Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing (Theoretical Physics), 1998

2nd Ph.D. Department of Physics, University of Illinois at Chicago (Experimental Biophysics), 2005


E-mail: phyyj@nus.edu.sg


Research Interests

Micromechanics of various DNA structures, their transitions and functions
DNA can form multiple structures to perform multiple biological functions. We have been investigating the stability of various important DNA structures, the factors that control the transition transform from one structure to another, and how the structures interact with their binding partners to perform the functions, at a single-DNA level.


Micromechanics of cytoskeleton proteins and their roles in mechanosensory processes of cells

Mechanical force is now acknowledged as a ubiquitous physiological factor controlling a variety of crucial biological functions. An important hypothesized mechanism is through force dependent changes in mechanosensory protein conformations that change their interactions with other cellular signaling proteins.  We have been testing this fundamental hypothesis at a single-protein level.


DNA packaging and gene regulations by major nucleoid associated proteins (NAPs) in bacteria

Bacterial genome is tightly packaged by roughly a dozen of abundant DNA architectural NAPs. Besides packaging DNA, NAPs also affect gene transcription. We have been studying the DNA binding modes of the major NAPs and how these binding modes are related to their gene regulation functions.


Single-stranded DNA (ssDNA) binding proteins and their functions

ssDNA binding proteins play critical roles in DNA replication and DNA damage repair. We have been investigating the binding and actions of major eukaryotic and prokaryotic ssDNA binding proteins on single ssDNA molecules.


Representative Publications

1. 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. 41:5263-5272.

2. 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.

3. 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. 41:924-932.

4. 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 coli during anoxia." Nucleic Acids Research. 41:746-753.

5. 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: 218102.

6. 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.

7. 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.

8. 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.

9. Fu, H.X., H Chen, X.H. Zhang, Y QU, J.F. Marko and J. Yan (2011). "Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching." Nucleic Acids Research 39: 3473-3481.

10. Fu, H.X., H.Chen, J.F. Marko, and J. Yan (2010). "Two distinct overstretched DNA states." Nucleic Acid Research 38: 5594-5600.

11. 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.


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