img018 - Blackboard Learning System node for.7 1 two...

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Unformatted text preview: 10/27/2010 Blackboard Learning System node for .7 .......... 1. two unrelated and/or synthetic DNA molecules can form a duplex (,th one .......... 2. the sequences need not be completely identical bmpcw ’5 nwllEd ............... a. n'ismatch lowers Tm (approximately 1 0C for every 1% mismatch) mom {7, Ca .96!" .......... 3. a crucial tool in molecular biology _ _ (9%th t [m 10 V. ............... a. for example, annealIng of ten’plate and pnmer for DNA sequencmg ’Mf' “J 4) Forces holding a duplex together: is it H-bonds or base stacking? WWTMM ..... a) Compare folded to unfolded state mmd .......... 1. polar solvent. stacking important, H-bonds unin'portant .......... 2. nonpolar solvent. H—bonds irrportant, stacking unimportant ..... b) Depéndence of Tm on %GC (Saenger, page 149) .......... 1. not 3 H— bonds for G=C versus 2 for A=T Tm( in °C)— " 0 Hi (‘73 GC) .......... 2. rather, more base overlap (stacking interaction) for G=C versus A=T ..... c) Dramatic Tm increase in a helix composed of "expanded" WC basepairs .......... 1. Liu et al., 2003, Science 203: 868-871 ..... d) Nature of base stacking interaction .......... 1. van der Waals interactions .......... 2. hydrophobic effect Rmarurm‘on: optimum (gnaw/MW ”“203 . 1’ 00 6C? TertIarv Structure of DNA bum/4W 0660 3 b pal»? b 5) Supercoiling Fallér) MOW Wmséac 0N0 CW ..... a) Requirement Ir 461mm tr (2% 0"- nor H 10071ng ha! "y 709 .......... 1. closed circular duplex (Watson and Crick) or nonmiarmvmr. 00V) polar .......... 2. some other constraint, such as a loop fom'Ied by bound protein noggin :andCK/y _____ b) Temino|ogy WWW mom willJl/(grelax .......... 1. relaxed: "correct" nurrber of turns normal )3 rm ~ fi? .......... 2. negatively supercoiled = undenNound: too few tums expandedfgliltdcofldfi , .......... 3. positively supercoiled = ovenNound: too many turns ;J ..... c) Topology (Figures 11. 22 and 11.. 24) Closed OLA/MEI in Spac’c @ u .......... 1. L = linking nurrber (nurrber of times Watson is interlocked with Crick) STCuCW WM“ ............... a. L > 0 for right- -handed rotation (as in relaxed A or B DNA) Wary me/m’agfi ............... b. L < 0 for left-handed rotation (as in relaxed 2 DNA) .......... 2. T = twist (roughly the nunber of helical turns) ............... a. T > 0 for right-handed turns (as in A or B DNA) pOsIhI/e moist ............... b. T < 0 for left-handed tums (as in 2 DNA) fit“ cam/c WK!“ .......... 3. W = writhe (roughly the nurrber of supercoils) KbO'lC of an? ............... a. W > 0 for left-handed mm supercoils (see below) ............... b. w < 0 for right-handed plectgnen'ic supercoils (see below) .......... 4. L = T + W ............... a. L is an integer and invariant unless a covalent bond is broken ............... b. T and W are continuous variables and vary continuously .......... 5. AL = AT + AW, where gyrcga #1777901”ch ............... a. AL=L2 L1, AW g’(SWZ- W1, andAT== T2- T1 ----- ., We "are”; .......... 1. type I topOIsomerases ............... a. mnechanism involves a transient single-strand break frTP) ................. the other single strand is passed through the break '\. ................. G2 or the nicked stand rotates around the intact strand mOYC atom, ............... b. linking number changes in steps of 1 t no EMUQW .......... 2. type II topoisornerases ............... a. mechanism involves a transient double-strand break .................... another double strand is passed through the break ............... b. linking nun'ber changes in steps of 2 .......... 3. DNA gyrase, an energy- dependent t1Lpe.11—topoisormra_s_e~ ............... a. Wes negative supercoils at the expense of ATP hydrolysis ..... e) Superhelix density (Figure 11. 24) 7 moms sum/cor 15 (V ...uga.edu/.../coba|tMainFrame.dowebct 4/6 ...
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