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Major and minor grooves

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

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Major and minor grooves

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  1. 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 • Regulatory proteins (transcription factors) can recognize the pattern of bases and H-bonding possibilities in the major groove

  2. 12.3 Denaturation of DNA See 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 light • When T is lowered, the absorbance drops, reflecting the re-establishment of stacking

  3. Secondary Structures in DNA • Slipped strand • Cruciform • Triple helix • All sequence dependant

  4. Slipped Strand Structures • 5′-TACGTACGTACGTACG-3′ • Tandem or direct repeat? • TACG

  5. Cruciform Structures • Paired stem loops • They 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 microscopes

  6. Inverted Repeat

  7. Triple Helix DNA • A third strand of DNA joins the first two to form triplex DNA. • Occurs at purine–pyrimidine stretches in DNA and is favoured by sequences containing a mirror repeat symmetry

  8. Hoogsteen AT and GC base pairs • The purine strand of the Watson–Crick duplex associates with the third strand through Hoogsteen hydrogen bonds in the major groove. • Discovered by KarstHoogsteen) • Different patterns of hydrogen bonding compared with Watson–Crick base pairs • In the Hoogsteen AT pair, the adenine base is rotated through 180° about the bond to the sugar, and the HoogsteenGC pair only forms two hydrogen bonds, compared with three in the Watson–Crick GC pair. • Hoogsteen GC base pairs are not stable at the neutral pH of cells (pH 7–8). 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 4–5). • Hoogsteenbase 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.

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