Introduction to Single - Dna Micromechanics ( June 2 , 2005 )

15 2.2.6. Permanent sequence-driven bends 16 2.3. Stretching out the double helix 17 2.3.1. Small forces (< k B T /A = 0.08 pN) 18 2.3.2. Larger forces (> k B T /A = 0.08 pN) 18 2.3.3. Free energy of the semiflexible polymer 19 2.3.4. Really large forces (> 10 pN) 21 3. Strand Separation 22 3.1. Free-energy models of strand separation 23 3.1.1. Sequence-dependent models 24 3.1.2. Free energy of internal 'bubbles' 25 3.1.3. Small internal bubbles may facilitate sharp bending 26 3.2. Stretching single-stranded nucleic acids 26 3.3. Unzipping the double helix 29 3.3.1. Effect of torque on dsDNA end 31 3.3.2. Fixed extension versus fixed force for unzipping 32 4. DNA Topology 33 4.1. DNA supercoiling 33 4.1.1. Twist rigidity of the double helix 33 4.1.2. Writhing of the double helix 34 4.1.3. Simple model of plectonemic supercoiling 36 4.2. Twisted DNA under tension 39 4.3. Forces and torques can drive large structural reorganizations of the double helix 41 4.4. DNA knotting 42 4.4.1. Cells contain active machinery for removal of knots and other entanglements of DNA 43 4.4.2. Knotting a molecule is surprisingly unlikely 43 4.4.3. Condensation-resolution mechanism for disentangling long molecules 44 5. DNA-Protein Interactions 45 5.1. How do sequence-specific DNA-binding proteins find their targets? 46 5.1.1. Three-dimensional diffusion to the target 46 5.