A very simplistic approach to explain B-DNA structure variations during the formation of protein-DNA complexes.

1. Helix Structure And Molecular
Recognition By B-DNA
A heap of paradoxes

2. Characteristics of B-DNA
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It is a right handed helix.
Angle of helical twist per turn is 35.9°.
BP/turn = 10.5
Diameter = 20 Å
The major groove, is 22 Å wide and the other,
the minor groove, is 12 Å wide.

3. Questions that arise…
• Do local helical structures of DNA depend on
local base pair sequence ?
• To map the DNA structural deviations, which
sample should we use? Aq. solution or DNA
crystals ?
• If GC base pairs make DNA more stable then
why does it have a lot of AT BPs ?

4. Dodecamer Decade
• CGCxxxxxxGCG
• All the possible nucleotides with this
sequence were synthesized, crystallized and
subjected to X-ray crystallography.
• To chalk out rules for helical twist, roll angle,
rise, slide, propeller twist etc. on the basis of
data thus obtained.
• This data could be used to distinguish
different forms and conformations of DNA.

6. Calladine’s Rules
• It was realized that value of a helix parameter
could be affected by preceding or following
steps.
• It was discovered that B-DNA decamers, when
crystallized, would behave a very
long, repetitive helix.
• It exhibited different local parameters in
different crystalline environment.

7. • What is going on ? Did DNA not have a fixed
structure ?
• Are X-ray crystallography data accidents
produced by local crystal packing forces ?
• Is DNA duplex just a shapeless mass of
Brownian spaghetti ?

8. Sequence Based Differential
Deformability
• The deviation range exhibited by a
particular helical parameter depends
on the sequence.
• But the exact conformation depends
on the crystalline environment, or
the environment that an
approaching protein creates.

9. Molecular Properties: inferences
• Sugar pucker is C2’-endo. But it deviates and
goes as far as C4’-exo. On the other hand ADNA sugar pucker is more clustered around
C3’-endo.
• This shows that B-DNA is more malleable than
other structural alternatives. Due to less
rigidity, it is more suitable for involvement in
molecular recognition process.

11. Contd…
• AT pairs show more variability in propeller
twist. (Double H-bond)
• Similarly, minor grooves width is more
variable in regions of successive AT base pairs.
• Mean twist angle is 36 . But varies from 20 to
55 .
• Bending of B-DNA duplex are caused by Roll.
(Tilt is rather unfavorable).

12. Sequence Factor
• Pyrimidine = Y, Purine = R
• Y-R steps
• R-Y / R-R steps

13. Correlation (Local roll/twist/slide/tilt)
• Heterogeneous step ending in A, display negative
correlation between slide and roll, twist and roll;
and positive correlation between slide and twist.
• In Y-R steps, large slide or twist do not favor a
large positive roll. (except C-G)
• R-Y steps prefer negative values of slide and twist.
• The correlation plots have proved out to be
similar to those from crystallography analysis.

14. Protein-DNA complexes
Four Classes (Describe):
• HTH proteins
• Zn-binding proteins
• bZIP, bHLH
• Others

15. CAP-DNA

17. Conclusions
Bending
• Bends are the result of ROLL (mostly).
• Bend for a protein can be achieved by (kinks,
slow progression).
• Role of major groove and minor groove.
• Y-R steps are most prone to roll/slide bending.
• R-R steps are very stiff, especially A-A.

18. Base Occurrence
• A-A step is most common of all (16%).
• 55% of these are poly-A runs.
• Preference for A-A is a consequence of natural
selection for a stabilizing structural element.
• By contrast G-G base pairs are rare and less
compatible with complexes involving
Sequence Reading.
• [These are all probabilistic rules, not
hueristic.]