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BMCB625 Advanced Topics in Molecular Biology


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General Info

  • Spring 2007
  • Location: BRB 603. Wednesdays from 9:30 - 11:30 (practice and review session) and Thursdays (The Real Thang) from 10:30 - 12:30
  • How the Class Works

Week-by-Week Schedule Summary

Date Presenters Topic Evaluator/MC/Faculty
April 4 Hoatlin/Dresbeck Org Meeting NA
April 12 Chris & Maureen BMCB625:DNA Replication JF/CP/(Hoatlin&Thayer)
April 19 Chayne & Larry BMCB625:DNA Replication (New components) JL/CS (Hoatlin/Thayer)
April 26 Jeremy & Chayne BMCB625: noncoding RNA (Xist) LG/JF (Thayer)
May 2 (Wed) BMCB625: Bringing it all together - DNA replication and NC RNA
May 17 Jon (Happy Birthday) & Jeremy BMCB625:Nucleosome Coding CS/MN(Lundblad?)
May 24 Larry & Jon BMCB625:Helicases MN/JL (Hoatlin/Chapman)
May 31 Mahta & Chris BMCB625:Exon Jxn Complex CP/LG(Rotwein/Landfear?)
June 7 Chris BMCB625:Mathematics in Biology (Chayne, MC) (Shinde?, Farrens?)
June 7 Chayne BMCB625:DNA Gyrase (Chris, MC) (Hoatlin/Thayer/Smolik)
June 13 Mahta BMCB625:Noncoding Y RNA (Jeremy, MC) (Thayer/Rotwein?)
June 13 Jeremy BMCB625:ncRNA (Mahta, MC) (Thayer)
June 14 Larry BMCB625:pol-Y (Excision Repair) (Jon, MC) (Hoatlin/Lloyd/McCullough)
June 14 Jon BMCB625:Topo (Larry, MC)

Proposed Papers


Enlist a faculty mentor
send them the paper
make sure the date works
vote by wiki?
Make sure there is consensus (excitement) among remaining class members about the proposed paper
again, vote can be done on wiki


Proposed Paper for Discussion--Contact Chayne for inquiries

  1. Nöllmann M, Stone MD, Bryant Z, Gore J, Crisona NJ, Hong SC, Mitelheiser S, Maxwell A, Bustamante C, and Cozzarelli NR. Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol. 2007 Apr;14(4):264-71. DOI:10.1038/nsmb1213 | PubMed ID:17334374 | HubMed [Nollman]


E. coli DNA gyrase uses the energy of ATP hydrolysis to introduce essential negative supercoils into the genome, thereby working against the mechanical stresses that accumulate in supercoiled DNA. Using a magnetic-tweezers assay, we demonstrate that small changes in force and torque can switch gyrase among three distinct modes of activity. Under low mechanical stress, gyrase introduces negative supercoils by a mechanism that depends on DNA wrapping. Elevated tension or positive torque suppresses DNA wrapping, revealing a second mode of activity that resembles the activity of topoisomerase IV. This 'distal T-segment capture' mode results in active relaxation of left-handed braids and positive supercoils. A third mode is responsible for the ATP-independent relaxation of negative supercoils. We present a branched kinetic model that quantitatively accounts for all of our single-molecule results and agrees with existing biochemical data.


  • make sure each of you has a slot as presenter 1 and 2.