Dr. P. Shing Ho Laboratory

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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

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.

External links