Major and minor grooves

3. 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

6. 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

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

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

12. 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

13. Inverted Repeat

14. 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

16. 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.