Helix Structure And Molecular Recognition By B-

DNAA heap of paradoxes

Characteristics of B-DNA

• 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.

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 ?

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.

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.

• 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 ?

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.

Molecular Properties: inferences

• Sugar pucker is C2’-endo. But it deviates and goes as far as C4’-exo. On the other hand A-DNA 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.

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).

Sequence Factor

• Pyrimidine = Y, Purine = R• Y-R steps• R-Y / R-R steps

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.

Protein-DNA complexesFour Classes (Describe): • HTH proteins• Zn-binding proteins• bZIP, bHLH• Others

CAP-DNA

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.

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.]