Question

1. What was the significance of Photo 51?

2. What causes there to be a major and minor groove? What is the difference?

3. Which groove contains more “information” and why? How do proteins interact specifically with this DNA groove, as when a zinc finger crosses the groove?

4. Which of the following base pairs could proteins distinguish, and why?

a. Major groove base pairs (GC/CG, AT/TA, GC/TA, GC/AT)

b. Minor groove base pairs (GC/CG, AT/TA, GC/TA, GC/AT)

5. Where do you find A DNA, B DNA, Z DNA, and quadruplex DNA?

Answer 1

1.Photograph 51 is the nickname given to an X-ray diffraction image of crystallized DNA taken by Raymond Gosling in May 1952, working as a PhD student under the supervision of Rosalind Franklin, at King's College London in Sir John Randall's group. It was critical evidence in identifying the structure of DNA.

2.The attachment of bases to the backbone sugars through glycosidic bonds is asymmetrical. This results in the formation of two different grooves on opposite sides of the base pairs, the major and minor grooves .These grooves acts as base pair recognition and binding sites for proteins.

Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other, the grooves are unequally sized. One groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide. The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.This situation varies in unusual conformations of DNA within the cell, but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.

3. Major groove is information rich.The edges of each base pair are exposed in the major and minor grooves, creating
a pattern of hydrogen-bond donors and acceptors and of hydrophobic groups (allowing for van derWaals interactions) that identifies the base pair. The edge of an A:T base pair displays the following chemical groups in the following order in the major groove: a hydrogen-bond acceptor (the N7 of adenine), a hydrogen-bond donor (the exocyclic amino group on C6 of adenine), a hydrogen-bond acceptor (the carbonyl group on C4 of thymine), and a bulky hydrophobic surface (the methyl group on C5 of thymine). Similarly, the edge of a G:C base pair displays the following groups in the major groove: a hydrogen-bond acceptor (at N7 of guanine), a hydrogen-bond acceptor (the carbonyl on C6 of guanine), a hydrogen-bond donor (the exocyclic amino group on C4 of cytosine), and a small nonpolar hydrogen (the hydrogen at C5 of cytosine).

Thus, there are characteristic patterns of hydrogen bonding and of overall shape that are exposed in the major groove that distinguish an A:T base pair from a G:C base pair, and, for that matter, A:T from T:A, and G:C from C:G. We can think of these features as a code in which A represents a hydrogen bond acceptor , D hydrogen bond donor, M a methyl group, and H a nonpolar hydrogen.

In such a code, ADAM in the major groove signifies an A:T base pair, and AADH stands for a G:C base pair. Likewise, MADA stands for a T:A base pair, and HDDA is characteristic of a C:G base pair. In all cases, this code of chemical groups in the major groove specifies the identity of the base pair. These patterns are important because they allow proteins to unambiguously recognize DNA sequences without having to open and thereby disrupt the double helix. Indeed,  a principal decoding mechanism relies on the ability of amino acid side chains to protrude into the major groove and to recognize and bind to specific DNA sequences.

4. a. Major groove base pairs (GC/CG, AT/TA, GC/TA, GC/AT) could proteins distinguish because they can form more hydrogen bonds to interact with DNA.

5.

The B form, which is observed at high humidity, most closely corresponds to theaverage structure of DNA under physiological conditions. It has 10 bp per turn and a wide major groove and a narrowminor groove. TheAform, which is observed under conditions of low humidity, has 11 bp per turn. Its major groove is narrower and much deeper than that of the B form, and its minor groove is broader and shallower. The vast majority of the DNA in the cell is in the B form, butDNAdoes adopt the A structure in certain DNA–proteincomplexes. In addition, the A form is similar to the structure that RNA adopts when double-helical.

Z-DNA

In solution, alternating purine–pyrimidine residues assume the left-handed conformation only in the presence of high concentrations of positively charged ions (e.g., Na+) that shield the negatively charged phosphate groups. At lower salt concentrations, they form typical right-handed conformations. The physiological significance of Z DNA is uncertain, and left-handed helices probably account at most for only a small proportion of a cell’s DNA.