major and minor grooves

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Major and minor grooves. The "tops" of the bases (as we draw them) line the "floor" of the major groove The major groove is large enough to accommodate an alpha helix from a protein - PowerPoint PPT Presentation

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Major and minor groovesThe "tops" of the bases (as we draw them) line the "floor" of the major groove The major groove is large enough to accommodate an alpha helix from a protein Regulatory proteins (transcription factors) can recognize the pattern of bases and H-bonding possibilities in the major groove 13

12.3 Denaturation of DNASee Figure 12.17 When DNA is heated to 80+ degrees Celsius, its UV absorbance increases by 30-40% This hyperchromic shift reflects the unwinding of the DNA double helix Stacked base pairs in native DNA absorb less lightWhen T is lowered, the absorbance drops, reflecting the re-establishment of stacking16

Secondary Structures in DNASlipped strandCruciformTriple helixAll sequence dependant

Slipped Strand Structures5-TACGTACGTACGTACG-3Tandem or direct repeat?TACG

Cruciform StructuresPaired stem loopsThey have been characterized in vitro for many inverted repeats in plasmids (small circular DNA) and bacteriophages. Inverted repeats are base sequences of identical composition on the complementary strands.They read exactly the same from 5 3 on each strand (in other words, the sequence reads the same from left to right as from right to left. Also called palindromes because of their similarity to a word or phase that reads identically when spelled backward.Seen under electron microscopesInverted Repeat

Triple Helix DNAA third strand of DNA joins the first two to form triplex DNA. Occurs at purinepyrimidine stretches in DNA and is favoured by sequences containing a mirror repeat symmetry

Hoogsteen AT and GC base pairs The purine strand of the WatsonCrick duplex associates with the third strand through Hoogsteen hydrogen bonds in the major groove. Discovered by Karst Hoogsteen) Different patterns of hydrogen bonding compared with WatsonCrick base pairs In the Hoogsteen AT pair, the adenine base is rotated through 180 about the bond to the sugar, and the Hoogsteen GC pair only forms two hydrogen bonds, compared with three in the WatsonCrick GC pair.Hoogsteen GC base pairs are not stable at the neutral pH of cells (pH 78). One of the nitrogens on the cytosine must have a hydrogen added to it for this type of base pair to form, and this protonation requires a lower pH (pH 45). Hoogsteen base pairs have gained importance recently because they are occasionally found in complexes of DNA with anticancer drugs and they show up in triple helices associated with genetic disease.