B-form Most common DNA conformation in vivo Narrower, more elongated helix than A. Wide major groove easily accessible to proteins Narrow minor groove Favored conformation at high water concentrations (hydyration of minor groove seems to favor B-form) Base pairs nearly perpendicular to helix axis Sugar pucker C2-endo Note that the major groove (at the top, when you have just clicked the button) is wide and easily accessible. Now the bases are easier to see. Notice how they are stacked upon each other and are nearly perpendicular to the axis of the double helix. Note also that the backbone forms a smooth, continuous curve. Zoom in on a few base pairs with this button. Hydrogen bonds between the bases are shown in white. You are looking into the major groove. Each base pair stacks on the next similarly, as shown from this view. A-form DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently. DNA is usually found in the B form under physiological conditions. Sometimes kinks are found in the B helix at transcriptional control regions. These kinks can either be intrinsic to the DNA sequence or caused by transcription factor binding. A-form Most RNA and RNA-DNA duplex in this form shorter, wider helix than B. deep, narrow major groove not easily accessible to proteins wide, shallow minor groove accessible to proteins, but lower information content than major groove. favored conformation at low water concentrations base pairs tilted to helix axis Sugar pucker C3-endo (in RNA 2-OH inhibits C2-endo conformation) Note that the major groove (at the top, when you have just clicked the button) is very deep. Notice how they are stacked upon each other but not perpendicular to the axis of the double helix. They are also displaced to the side of the axis. The result is a wide, short helix. Note also that the backbone forms a smooth, continuous curve. Zoom in on a few base pairs with this button Hydrogen bonds between the bases are shown in white. You are looking into the major groove. Each base pair stacks on the next similarly, as shown from this view. B-DNA also stacks in this way, but compare this with Z-DNA, which behaves much differently. Essentially all helical RNA is in A form, but DNA can also be found in A form under certain conditions (particularly in RNA-DNA hybrids). The 2-OH of ribose (shown in white in this view) favors the C3-endo sugar pucker necessary for A-form geometry. The O2 stericly disfavors the C2-endo conformation favored in B-DNA. Z-form Helix has left-handed sense Can be formed in vivo, given proper sequence and superhelical tension, but function remains obscure. Narrower, more elongated helix than A or B. Major groove not really groove Narrow minor groove Conformation favored by high salt concentrations, some base substitutions, but requires alternating purine-pyrimidine sequence. N2-amino of G H-bonds to 5 PO: explains slow exchange of proton, need for G purine. Base pairs nearly perpendicular to helix axis GpC repeat, not single base-pair P-P distances: vary for GpC and CpG GpC stack: good base overlap CpG: less overlap. Zigzag backbone due to C sugar conformation compensating for G glycosidic bond conformation Conformations: G; syn, C2-endo C; anti, C3-endo
Posted on: Sun, 19 Oct 2014 06:32:28 +0000
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