Dr. P. Shing Ho Laboratory
From Christoph's Personal Wiki
The Dr. P. Shing Ho Laboratory is where I did scientific research from May 2000 – September 2004.
Note: Dr. Ho was a Professor & Chair of the Department of Biochemistry & Biophysics at Oregon State University while I did my research from 2000 to 2004. He has since moved to Colorado State University as Professor & Chair of the Department of Biochemistry & Molecular Biology.
Research topics
- Z-DNA
- ZHunt Online Server
- Topoisomerase
- DNA topology
- DNA supercoil
- Linking number
- DNA Gyrase — adds negative supercoils to DNA using ATP hydrolysis for energy (9 kcal/mole). 200bp of DNA wrap around the gyrase holoenzyme molecule, ATP is bound, and each strand is cut (staggered cuts) and covalently linked to different tyrosines to "anchor" the DNA.
- DNA gyrase inhibitors:
- - nalidixic acid (prevents strand cutting and rejoining); and
- - novobiocin (blocks ATP binding)
- CCAAT-Enhancer-Binding Proteins
- Macrophage Colony-Stimulating Factor
- Möbius strip
Results
The research I did in this laboratory yielded a paper published and a Web Server:
- Programmer; May 2000-September 2004 (note: Website by Sandor Maurice)
References
- P. Christoph Champ, Sandor Maurice, Jeffery M. Vargason, Tracy Camp, and P. Shing Ho (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research, 32(22):6501-6510 DOI:10.1093/nar/gkh988 . [HubMed]
- Citations:
- → Liu H, Mulholland N, Fu H, Zhao K (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. Mol Cell Biol, 26(7):2550-9.
- → Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature, 437:1183-1186.
- → Kwon JA, Rich A (2005). Biological function of the vaccinia virus Z-DNA-binding protein E3L: Gene transactivation and antiapoptotic activity in HeLa cells. Proc Natl Acad Sci USA, 102:12759-12764.
Further reading
- Ho PS (1994). The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proc Natl Acad Sci USA, 91(20):9549-9553.
- Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J, 5(10):2737-2744.
