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

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

Secondary Structures in DNA

• Slipped strand• Cruciform• Triple helix• All sequence dependant

Slipped Strand Structures

• 5 -TACGTACGTACGTACG-3′ ′• Tandem or direct repeat?• TACG

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

Inverted Repeat

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

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 Karst Hoogsteen) • 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 Hoogsteen GC 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).

• 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.