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).