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img016 - Blackboard Learning System 1 shorter fragments...

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Unformatted text preview: 10/27/2010 Blackboard Learning System .......... 1. shorter fragments migrate faster .......... 2. sequence is read from the bottom of the gel to the 'top .......... 3. sequence obtained is the 5'- 3' sequence of the newly synthesized strand .......... 4. this sequence is the reverse con'plement of the template sequence ..... e) High— throughput variants (1 gigabase/run) » V .......... 1. 454 (G&G4, page 319) .......... 3. Pacific Biosciences single molecule sequencing ............... a. wwwpac :sicosesceenies corr tideo rightmi PIl'an - Secondary Structure of DNA vamdm WaouU 6) All Nucleic Acid Secondary Structure is Helical (Figure 11.5) (byway? 03mm ..... a) Extended ladder with perpendicular bases is energetically unfavorable, because .......... 1. hydrophobic surfaces of the bases are in contact with water ..... b) Helix formation allows base stackin (water Is expelled) 9 MM rcd» ..... c) Propellor twist (Figure 11.8) DWih'l'PX‘CLC Cl’f‘iOn 75 .......... 1. weakens H— bonding, but ASTO-C .......... 2. maximizes base stacking W ..... d) But why not an extended ladder with tilted bases?! .......... 1. stretched DNA (S-DNA) is proposed to have such a structure ............... a. Bustarnante et al, 2000, Curr. Op. Str. Biol. 10: 279-285 3W"? 0‘01 WW ............... b. mechanical stretching of single molecules ............... c. length increases to 1.7 X .......... 2. however, S— DNA reverts to a helix when tension is removed .......... 3. so S-DNA must be less stable than a helix Sugar + bCW‘L 7) Conformation of Nucleosides and NUCIEWTF W «Sui/L ..... a) Conformation aro rid the glycosid/c linkage is hindered (Figure 11. 4c) V .......... 1. pyrimidines. onfom'Iation only normal WT’M ............... a. 2- carborWl/rlepelled by ring oxygen .......... 2. purines: anti preferred but syn possible ’q Wolff? Obnm ..... b) Furanose puckering (Figure 11.4b, Handout Saenger Figure 9-3) We on W .......... 1. envelope conformations favored SWW ............... a. endo: nonplanar atom on same side of the furanose ring as CS' “M“ ............... b. exo: nonplanar atom on opposite side of the furanose ring from CS' W .......... 2. nonplanar atom usually C2‘ or C3' ............... a. C2' endo, C2' exo, C3' endo, C3' exo .......... 3. C2' endo leads to B-family helices; C3‘ endo to A-family helices .......... 4. DNA: A- and B—family helices are both possible .......... 5. RNA: only A-family helices are possible ............... a. steric hindrance of 2'-OH excludes RNA from B-family helices 8) The ABZ's of DNA Secondary Structure ZlS l-CH "hand-60‘ ..... a) A, g, C, D, : fiber—diffraction at different relative humidities, single crystal .......... 1. A at <100% relative humidity, B at 100% (fully hydrated) .......... 2. C, D, : minor forms ..... b) ;: X-ray crystal structure of CGCGCG 0mg Comgujfimn 123%,“; EQNM .......... 1. Z-DNA requires alternating pyrimidine~purine .......... 2. named for zig-zag path of sugar phosphate backbone .......... 3. "The general response to this unusual structure was amazement, coupled ............... with skepticism." Alexander Rich, 2004, The Excitement of Discovery, ............... Annu. Rev. Biochem. 73: 1-37. ..... c) Parameters of A—, B-, and Z—DNA (Table 11.1) W .......... 1. note: Z-DNA has C2' endo at C, C3' endo at G ..... d) Structure of A-, B-, and Z-DNA (Figure 11.9 and Lehninger Figure 12-18) ..... e) Major/minor grooves of B—DNA (Figure 11.7) Map? 661 96 —-7 morgroove .......... 1. major/minor edges of WC base pairs Minor cage «4 minor 01:21ij ...uga.edu/.../cobaltMaInFramedowebct l’YiOYCSCCl Ml”? C U WU Ui’l rt 10501” C3' 30% 2/6 ...
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