Major and minor grooves
description
Transcript of 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
• 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.