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Lecture11_NABPty2012 (1)

Increasing energy empty orbitals strong absorption

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Unformatted text preview: 60 nm interacting bases weaker band near 260 nm individual base strong band near 260 nm Summary of the main structural features of B-form DNA •Right-handed helix •Two antiparallel strands held together by Watson-Crick hydrogen bonds •Pitch (repeat length) = 34 Å (3.4 nm) •36o rotation between residues •Helix diameter of 20 Å (2.0 nm) •Wide major groove, narrow minor groove •Chargaff’s Rules: A = T; G = C •Charged phosphates •Bases in anti configuration •The strands separate at high temperatures •The solution structure is dynamic Tautomeric forms of G & T can cause mutations due to mis-pairing during DNA replication O OH C HN C H2N-C C N C N CH N Guanine (keto form) N C H2N-C C N N CH N Guanine (enol form) xx O C HN O C N OH C C CH3 CH Thymine (keto form) N O C C CH3 CH N Thymine (enol form) The ring NH atoms of G and T have pKa values of about 9. At physiological pH, about 99% of the base is in the keto form and 1% in the enol form. Palindromic* sequences (inverted repeats) in DNA or RNA can form hairpin or cruciform structures 5’ TGCGATACTCATCGCA 3’ 3’ ACGCTATGAGTAGCGT 5’ inverted repeats in an antiparallel double helix C T A 5’ A T C G C A T A C T A G C G T A T C G C A 5’ hairpin 3’ Mirror repeats cannot form such structures. 3’ 3’ C T A G C G T C 5’ cruciform structure A C G C T A T G C G A T T G G A *A palindrome reads the...
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