RNA Folding and Therapeutics

 


Division of Chemistry and Biological Chemistry

School of Physical and Mathematical Sciences

Nanyang Technological University

 

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Publications

 

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Book Chapter

1.

Tinoco, I., Jr.,* Chen, G., and Qu, X. (2010) RNA reactions one molecule at a time, in RNA Worlds, (Gesteland, R.F., Cech, T.R., and Atkins, J.F., Eds.), Cold Spring Harbor Laboratory Press. Cold Spring Harb Perspect Biol. 10.1101/cshperspect.a003624  One of the Most Influential Books in Biology§

 

 

 

 

Journal papers

20

Xing Ma,= Gitali Devi,= Qiuyu Qu, Desiree-Faye Kaixin Toh, Gang Chen,* Yanli Zhao,* (2014) Intracellular Delivery of Antisense Peptide Nucleic Acid by Fluorescent Mesoporous Silica Nanoparticles, Bioconjugate Chem, 25, 1412-20. (= These authors contributed equally to this work)

 

 

19.

 

Gitali Devi,= Yuan Zhou,= Zhensheng Zhong,= Desiree-Faye Kaixin Toh,= and Gang Chen,* (2014) RNA Triplexes 每 From Structural Principles to Biological and Biotech Applications. Wiley Interdiscip Rev RNA, In press. (= These authors contributed equally to this work)

 

 

 

18.

 

Gitali Devi, Zhen Yuan, Yunpeng Lu, Yanli Zhao,* and Gang Chen,* (2014) Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes. Nucleic Acids Res, 42, 4008-18.

 

 

17.

Yuan Zhou, Elzbieta Kierzek, Zi Ping Loo, Meraldo Antonio, Yin Hoe Yau, York Wieo Chuah, Susana Geifman-Shochat, Ryszard Kierzek,* and Gang Chen,* (2013) Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides. Nucleic Acids Res 41, 6664-73.

 

 

RNA triplex.tif

 

 

 

16.

Chen, G., Chang, K.-Y., Chou, M.-Y., Bustamante, C., and Tinoco, I., Jr.* (Aug 2009) Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of 每1 ribosomal frameshifting. Proc. Natl. Acad. Sci. USA 106(31), 12706-11. (Cover Highlight and In This Issue Highlight)

 

 

 

15.

Chen, G., Kennedy, S.D., and Turner, D.H.* (Jun 2009) A CA+ pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops. Biochemistry 48(24), 5738-52.

 

TOC for website CA.tif

 

 

 

14.

Chen, G., Wen, J.-D., and Tinoco, I., Jr.* (Dec 2007) Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA 13(12), 2175-88. PDF

 

 

 

 

13.

Chen, G., Kierzek, R., Yildirim, I., Krugh, T.R., Turner, D.H.,* and Kennedy, S.D. (Jun 2007) Stacking effects on local structure in RNA: Changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs. J. Phys. Chem. B 111(24), 6718-27. PDF   Supporting Information  2O81  2O83 

 

TOC for website iGiC.tif

 

 

 

 

12.

Shankar, N., Kennedy, S.D., Chen, G., Krugh, T.R., and Turner, D.H.* (Oct 2006) The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50S ribosomal subunits. Biochemistry 45(39), 11776-89. (Listed as one of fifteen "Hot Articles" in Nov. 2006 in Biochemistry) PDF   Supporting Information  2H49

 

 

 

11.

Chen, G., Kennedy, S.D., Qiao, J., Krugh, T.R., and Turner, D.H.* (Jun 2006) An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA. Biochemistry 45(22), 6889-903.  PDF   Supporting Information  2DD1  2DD2  2DD3

 

TOC for website alternating AA.tif

 

 

 

10.

Chen, G., and Turner, D.H.* (Mar 2006) Consecutive GA pairs stabilize medium-size RNA internal loops. Biochemistry 45(12), 4025-43 (Listed as one of four "Hot Articles" in Mar. 2006 in BiochemistryPDF   Supporting Information

 

TOC for website consecutive GA.tif

 

 

 

9.

Chen, G., Znosko, B.M., Kennedy, S.D., Krugh, T.R., and Turner, D.H.* (Mar 2005) Solution structure of an RNA internal loop with three consecutive GA pairs. Biochemistry 44(8), 2845-56 (Listed as one of five "Hot Articles" in Feb. 2005 in Biochemistry) PDF   Supporting Information  1XV0

 

TOC for website 3GA.tif

 

 

8.

Chen, G., Znosko, B.M., Jiao, X., and Turner, D.H.* (Oct 2004) Factors affecting thermodynamic stabilities of RNA 3 ℅ 3 internal loops. Biochemistry 43(40), 12865-76. PDF   Supporting Information

 

toc-for website.tif

 

 

 

7.

Cui, Y.,* Chen, G., Ren, J., Shao, M., Xie, Y., and Qian, Y.* (Apr 2003) Solvothermal syntheses of 汕-Ag2Se crystals with novel morphologies. J. Solid State Chem. 172(1), 17-21. PDF

 

 

6.

Cui, Y.,* Chen, J., Chen, G., Ren, J., Yu, W., and Qian, Y. (Apr 2001) Bis(2,2-bipyridine-N,N')tetra-µ-chloro-tetracopper(I). Acta Crystallogr. Sect. C-Cryst. Struct. Commun. 57, 349-51. PDF

 

 

5.

Shao, M., Mo, M., Cui, Y., Chen, G., and Qian, Y.* (Dec 2001) The effect of agitation states on hydrothermal synthesis of Bi2S3 nanorods. J. Cryst. Growth 233(4), 799-802. PDF

 

 

4.

Cui, Y.,* Ren, J., Chen, G., Qian, Y.,* and Xie, Y. (Mar 2001) A simple route to synthesize MInS2 (M = Cu, Ag) nanorods from single-molecule precursors. Chem. Lett., (3) 236-7. PDF

 

 

3.

Cui, Y.,* Ren, J., Chen, G., Yu, W., and Qian, Y. (Dec 2000) Poly[lead(II)-µ-4,4-bipyridine-N,N'-di-m-bromo]. Acta Crystallogr. Sect. C-Cryst. Struct. Commun. 56, E552-3. PDF

 

 

2.

Cui, Y., Chen, G., Ren, J., Qian, Y.,* and Huang, J.* (Sep 2000) Syntheses, structures and magnetic behaviors of di- and trinuclear pivalate complexes containing both cobalt(II) and lanthanide(III) ions. Inorg. Chem. 39(18), 4165-8. PDF

 

 

1.

Cui, Y.,* Zhang, X., Zheng, F., Ren, J., Chen, G., Qian, Y., and Huang, J. (Oct 2000) Two mixed-metal carboxylate-base adducts. Acta Crystallogr. Sect. C-Cryst. Struct. Commun. 56, 1198-200. PDF

 

 

 

 

Presentations:

17

Gang Chen (September 2014, Invited Talk) Targeting RNA structures by triplex formation. SELECTBIO conference: Enabling Genomic Technologies and Screening Asia, Biopolis, Singapore

16

Gang Chen (July 2014, Talk) Targeting RNA structures by triplex formation. The 3rd National Conference on Biophysical Chemistry (NCBPC3), Qingdao, P.R. China

15.

Chen, G. (December 2011, Talk) Force and Fluorescence Spectroscopy Studies of RNA and RNA-Protein Complex.  The Third Asian Spectroscopy Conference, Xiamen University, Xiamen, P.R. China

 

 

14.

Chen, G. (September 2010, Talk) Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of 每1 ribosomal frameshiftingDepartment of Chemistry, National University of Singapore, Singapore

 

 

13.

Chen, G., Chou, M.-Y., Chang, K.-Y., and Tinoco, I., Jr. (June. 2009, Poster) Triplex structures in an RNA pseudoknot enhance mechanical stability   and increase efficiency of 每1 ribosomal frameshiftingBay Area All RNA Meeting, University of California, San Francisco

 

 

12.

Chen, G., Chou, M.-Y., Chang, K.-Y., and Tinoco, I., Jr., (May 2009, Poster) Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of 每1 ribosomal frameshifting. Annual Meeting of the RNA Society, Madison, Wisconsin. (Selected as NSMB sponsored ※The Best Poster in Biophysics and Structural Biology§

 

 

11.

Chen, G., Chou, M.-Y., Chang, K.-Y., and Tinoco, I., Jr., (April 2009, Talk) Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of 每1 ribosomal frameshifting. RNA Club, Center for Molecular Biology of RNA, University of California, Santa Cruz

 

 

10.

Chen, G. (January 2009, Job Talk) Base triples in RNA pseudoknots modulate mechanical stability and 每1 ribosomal frameshifting efficiency. Department of Pharmaceutical Sciences, University of Nebraska Medical Center

 

 

9.

Chen, G., Wen, J.-D., and Tinoco, I., Jr. (February 2008, Poster) Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA.   Biophysical Society Meeting, Long Beach, CA 

 

 

8.

Chen, G., Wen, J.-D., and Tinoco, I., Jr. (December 2007, Poster) Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA.   Bay Area All RNA Meeting, University of California, San Francisco 

 

 

7.

Chen, G., Wen, J.-D., and Tinoco, I., Jr. (August 2006, Invited Talk) Mechanical manipulation of a pseudoknot from human telomerase RNA.  Turner Symposium, University of Rochester 

 

 

6.

Chen, G., Kennedy, S.D., Znosko, B.M., Jiao, X., Krugh, T.R., and Turner, D.H. (November 2005, Talk)  Expanded Sequence Dependence Improves Prediction of RNA Internal Loop Stability and NMR Reveals Molecular Recognition Interactions Accounting for Stability, Structure, and Dynamics. RNA Structure and Function Cluster of     University of Rochester

 

 

5.

Chen, G., Znosko, B.M., Kennedy, S.D., Jiao, X., Krugh, T.R., and Turner, D.H. (October 2005, Poster)  Improved Thermodynamic Model for Predicting RNA 3 ℅ 3 Internal Loops and NMR Structure of an Unusually Stable Loop with Three Consecutive Sheared GA Pairs.   Upstate New York NMR Symposium, Cornell University

 

 

4.

Wood, A., Chen, G., Krugh, T.R., and Turner D.H. (March 2005, Poster)  Thermodynamic Stability of Tetramer RNA Sequences in the Presence of Various Metal Cations.   American Chemical Society National Meeting, San Diego, CA

 

 

3.

Chen, G., Znosko, B.M., Kennedy, S.D., Jiao, X., Krugh, T.R., and Turner, D.H. (September 2004, Talk)  Thermodynamics and NMR of 3 ℅ 3 Internal Loops in RNA.   Biological Chemistry Cluster, University of Rochester

 

 

2.

Chen, G., Znosko, B.M., Kennedy, S.D., Jiao, X., Krugh, T.R., and Turner, D.H. (August 2004, Poster)  Improved Thermodynamic Model for Predicting RNA 3 ℅ 3 Internal Loops and NMR Structure of an Unusually Stable Loop with Three Consecutive Sheared GA Pairs.   Biological Chemistry Cluster, University of Rochester

 

 

1.

Wood, A., Chen, G., Krugh, T.R., and Turner D.H. (August 2004, Poster)  Thermodynamic Stability of Tetramer RNA Sequences in the Presence of Various Metal Cations.   NSF Research Experiences for Undergraduates program, University of Rochester