TJ Ha seminar

some short notes:

  • DNA bending: requires 30 KT to bend 100bp circle. But lots of structures (e.g. nucleosomes) bend DNA on this scale.
  • Looping time has a very weak length dependence.
  • Weak dependence is not surface induced (watch individual DNA in tethered vesicles). Looping time does depend strongly on sequence. DNA is indeed very flexible, not well described by worm-like chain. * nucleosome positioning sequences is among the most flexible. PolyA tracks (avoided by nuclesomes) are less flexible.
  • Bubbles, especially in the middle of the sequence, dramatically increase looping time.
  • Strong half of nucleosome unwinding loops much faster than weak half.
  • whole genome looping time / genetic map of DNA flexibility.
  • Local melting on short sequences allows a hinge for short strand to bend. loss in melting is made up by gain in sticky end binding.
  • use DNA melting under shear force vs. unzipping (or different combinations based on position of handles). Cells can break free if bond cannot hold more than 40 pN.
  • Notch not activated by soluble ligand. Force required?
  • What about processing in receiver cell? (e.g. Tom / neuralized).
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