Difference between revisions of "Dr. P. Shing Ho Laboratory"

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* [[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, and 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])
+
* '''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'', '''26(7)''':2550-9 .
+
*** 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.  
+
*** 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.
+
*** 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'', '''91(20)''':9549-9553.
+
* 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, and 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.
+
* 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.

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