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Slide 6 : A-DNA: 2´-OH prevents B-form adoption
Major groove deeper and less accessible Z-DNA: Zig-zag path
Alternating Pu-Pyr, e.g., Poly d[GC], Poly d[AC]
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Slide 8 : The primary difference between A and B helices lies
in the sugar ring conformation (pucker).
The sugars are C3'-endo in the A structure, but
C2'-endo in the B-form. => Distance between adjacent
phosphates on one strand is shortened in A-form.
Moreover, in A-DNA the base pairs are displaced
from the central helix axis toward the major groove.
In B-DNA, the base pairs are essentially centered
over the helix axis.
In Z-DNA, the syn and anti orientations alternate
(all anti in both A and B-forms).
The pyrimidine nucleotides are in the standard anti
conformation with C2'-endo sugar pucker, while the
purine residues are syn and contain C3'-endo
conformation.
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Slide 10 : Stabilization by:
Maximize base stacking
Minimize unfavorable clashes between functional
groups of neighboring nucleotides
Form cross-strand H-bonds
Twist
Propellar twist
Roll
Slide
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Slide 12 : Purine clash is pronounced in the minor groove at 5?Pu- 3?Py
steps (-NH2 groups of adjacent purines in opposite strands try
to occupy the same space)
To avoid—decrease propeller twist,
decrease slide, or
increase roll angle.
A-T base pair runs:
Propeller twist (~200) of A-T base pair flanked by A-T
Maximizes Pu-Pu stacking leading to helix stability.
Formation of additional forked H-bonds
(A bonded to T’s of both pair as well as of adjacent one)
Very rigid structure, not bendable.
Runs of A exceeding 10 bp are generally found only at
the ends of natural nucleosomes, where bending of the
DNA is at a minimum.
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Slide 14 : Runs of GC base pairs:
The GC base pairs are displaced by sliding from the
central helix axis to result in favorable purine-purine
stacking.
This creates an inner core similar to that in an
A-form helix.
This similarity between the structure of duplex DNA
containing runs of GC base pairs and the structure of
duplex RNA and RNA-DNA hybrids (which form
exclusively A-form helices) may explain the capacity
of some proteins to bind DNA, RNA, and hybrid helices.
Slide 15 : Typical right-handed stacking pattern of single stranded RNA. The bases are shown in gray, the phosphate atoms in yellow, and the riboses and phosphate oxygens in green.
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Slide 18 : H-DNA. (a) A sequence of alternating T and C residues can be considered a mirror repeat centered about a central T or C. (b) These sequences form an unusual structure in which the strands in one half of the mirror repeat are separated and the pyrimidine containing strand (alternating T and C residues) folds back on the other half of the repeat to form a triple helix. The purine strand (alternating A and G residues) is left unpaired. This structure produces a sharp bend in the DNA.
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Slide 24 : Linking Number (Lk): Number of times one DNA strand
crosses the other.
Cannot be changed unless DNA
backbone is broken.
Twist (Tw): Number of helical turns
Writhe (Wr): Number of times the DNA backbone
turns,
can be both +ve (positive supercoiling)
or, -ve (negative supercoiling)
Lk = Tw + Wr
? = ? Lk/ Lk0
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