Lecture2

Lecture2 - DNA structure: stability and flexibility 1 DNA:...

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1 DNA structure: stability and flexibility
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2 sequence-specific variation:  helical twist per base pair: 28°-42° significance for DNA binding proteins DNA: Structure, Flexibility and Strain
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3 A-form B-form Z-form
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4 QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. flexibility and rigidity of DNA 7 potential torsion angles Fig 23.6 Fig 23.5 χ  is constrained by the double helical structure B-DNA all nucleotides are in anti-conformation. The DNA helix constrains the torsion angles. The type of helix that DNA forms determines the torsion  angles.
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5 rib o s e  ring  puc ke rs :  - o ne  C  is  o ut o f pla ne  to  re lie ve  c ro wding - whe the r C 2’ o r C 3’ is  o ut o f pla ne  de te rm ine s o rie nta tio n o f the  pho s pha te  g ro ups - in B-DNA all ribo s e  ring s  a re  C 2’-e ndo   Discussion section:  nuc le o tide  c he m is try, to rs io n a ng le s , fle xib ility o f nuc le o tide  to  fo rm  a lte rna te  s truc ture s ba s e  pairing , ba s e  s ta c king , pro pe lle r twis t, hydro pho b ic  a nd io nic  inte ra c tio ns   Nucleotide sugar conformations A-DNA B-DNA
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6 Forces stabilizing the DNA helix 1. base pairing A-A A-T (Ho o g s te e n) C -T Watson-and-Crick non-Watson-and-Crick
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7 Forces stabilizing the DNA helix 2. base stacking 3. ionic interactions phosphate backbones repel each other monovalent ions in buffer provide some shielding,  but divalent ions (Mg2+, Mn2+, Co2+ bind phosphates specifically and  provide for effective shielding DNA is more stable in the presence of ions !
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tRNA rRNA Not all nucleic acids from neat double helices! the  c o m b ine d func tio n o f a ll fo rc e s  re s ults  in the s e  s truc ture s
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Lecture2 - DNA structure: stability and flexibility 1 DNA:...

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