307d

[[Image:307d.gif|left|200px]]<br /><applet load="307d" size="350" color="white" frame="true" align="right" spinBox="true"

caption="307d, resolution 1.850&Aring;" />

'''STRUCTURE OF A DNA ANALOG OF THE PRIMER FOR HIV-1 RT SECOND STRAND SYNTHESIS'''<br />

==Overview==

The non-self-complementary DNA decamer C-A-A-A-G-A-A-A-A-G/C-T-T-T-T-C-T-T-T-G is a DNA/DNA analogue of a portion of the polypurine tract or PPT, which is a RNA/DNA hybrid that serves as a primer for synthesis of the (+) DNA strand by HIV reverse transcriptase (RT), and which is not digested by the RNase H domain of reverse transcriptase following (-) strand synthesis. The same unusual conformation that eludes RNase H, thought to be a change in width of minor groove, may also be responsible for the inhibition of HIV RT by minor groove binding drugs such as distamycin and their bis-linked derivatives. The present X-ray crystal structure of this DNA decamer exhibits the usual properties of A-tract B-DNA under biologically relevant conditions: large propeller twist of base-pairs, narrowed minor groove, and a straight helix axis. Groove narrowing is fully developed in the A-A-A-A region, but not in the A-A-A region, which previous investigators have proposed as being too short to exhibit typical A-tract properties. The RNA/DNA hybrid produced by HIV reverse transcriptase during (-) strand synthesis presumably forms a "heteromerous" or H-helix with narrower minor groove than an A-helical RNA/RNA duplex. If the narrowing of minor groove in A-tract H-helices is comparable to that seen in A-tract B-helices, then the narrowed minor groove of the polypurine tract could make the second primer site both (1) impervious to RNase H digestion, and (2) susceptible to inhibition by minor groove binding drugs.

 

==About this Structure==

307D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=307D OCA].

 

==Reference==

Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis., Han GW, Kopka ML, Cascio D, Grzeskowiak K, Dickerson RE, J Mol Biol. 1997 Jun 27;269(5):811-26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9223643 9223643]

[[Category: Protein complex]]

[[Category: Cascio, D.]]

[[Category: Dickerson, R E.]]

[[Category: Grzeskowiak, K.]]

[[Category: Han, G W.]]

[[Category: Kopka, M L.]]

[[Category: b-dna]]

[[Category: double helix]]