Difference between revisions of "Dr. P. Shing Ho Laboratory"
From Christoph's Personal Wiki
| Line 4: | Line 4: | ||
* [[Z-DNA]] | * [[Z-DNA]] | ||
* [[Z-Hunt|ZHunt Online Server]] | * [[Z-Hunt|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) | ||
| + | * Möbius strip | ||
== Results == | == Results == | ||
| Line 11: | Line 20: | ||
== References == | == References == | ||
| − | * '''P. Christoph Champ''', Sandor Maurice, Jeffery M. Vargason, Tracy Camp, | + | * '''P. Christoph Champ''', Sandor Maurice, Jeffery M. Vargason, Tracy Camp, P. Shing Ho (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. [http://nar.oupjournals.org/cgi/content/abstract/32/22/6501 ''Nucleic Acids Research, 32(22):6501-6510'']. [[http://www.hubmed.org/display.cgi?uids=15598822 HubMed]] ([http://gac-web.cgrb.oregonstate.edu/zDNA/ The Online server of ZHunt can be found here]) |
** <u>Citations</u>: | ** <u>Citations</u>: | ||
| − | *** Liu H, Mulholland N, Fu H, Zhao K (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. ''Mol Cell Biol | + | *** 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 | + | *** 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 | + | *** 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 === | === 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 | + | * 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, | + | * 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 == | == External links == | ||
Revision as of 03:57, 13 September 2006
The Dr. P. Shing Ho Laboratory is where I did scientific research from May 2000 – September 2004.
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)
- 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, 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. [HubMed] (The Online server of ZHunt can be found here)
- 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.
- Citations:
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.
