Seth Blumberg, Feb 2009

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Seth Blumberg is a MD/PhD who is visiting Caltech on 23 Feb (Mon). Use this page to schedule a time to meet with him.

Schedule

  • 8:45a: Arrival and seminar setup
  • 9:00a: Seminar, 139 Moore
  • 10:00a: Niles Pierce (if no jury duty)
  • 10:45a: Richard Murray, 109 Steele
  • 11:30a: Open
  • 12:00p: Lunch (host: Paul and Erik) - meet at Ath
  • 1:30p: Shuki Bruck, 331 Moore
  • 2:15p: Paul Rothemund, 204 Moore
  • 3:00p: Erik Winfree, 204 Moore
  • 3:45p: Open (note: there is a faculty meeting from 4-5 pm)
  • 4:30p: Open (note: there is a faculty meeting from 4-5 pm)

Seminar

The Computational Landscape of DNA looping

Seth Blumberg, U. Michigan
9:00 am, 139 Moore

DNA loops form when a protein binds to two operator sites on the same DNA molecule. In the biological world, DNA looping provides an intriguing control mechanism for gene regulation, DNA packaging and other sub-cellular processes. DNA looping is affected by a variety of biochemical and mechanical factors including the strength of DNA-protein interactions, tension in the substrate DNA and intra-operator sequence. In principle, specific looping dynamics can be engineered by manipulating these biomechanical constraints. For instance, it seems plausible to create a tunable AND-XOR-OR gate using a two-loop system under various degrees of tension. Similarly, a multiple loop system can be tuned so that the preferred configuration is responsive to the concentration of looping protein. Besides speculating on the computational landscape of DNA looping, I will review my involvement in single-molecule experiments that characterize simple looping systems.