307d: Difference between revisions

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[[Image:307d.gif|left|200px]]<br />

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

<applet load="307d" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

caption="307d, resolution 1.850Å" />

'''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.

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://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=307D OCA].

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==

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Line 13:

[[Category: Protein complex]]

[[Category: Cascio, D.]]

[[Category: Dickerson, R.E.]]

[[Category: Dickerson, R E.]]

[[Category: Grzeskowiak, K.]]

[[Category: Han, G.W.]]

[[Category: Han, G W.]]

[[Category: Kopka, M.L.]]

[[Category: Kopka, M L.]]

[[Category: b-dna]]

[[Category: double helix]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on Thu ~~Nov 8 14~~:57:~~48 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:01:52 2008''

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@@ Line 1: / Line 1: @@
-[[Image:307d.gif|left|200px]]<br />
+[[Image:307d.gif|left|200px]]<br /><applet load="307d" size="350" color="white" frame="true" align="right" spinBox="true"
-<applet load="307d" size="450" 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.
+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==
-D 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=307D OCA].
+D 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==
@@ Line 14: / Line 13: @@
 [[Category: Protein complex]]
 [[Category: Cascio, D.]]
-[[Category: Dickerson, R.E.]]
+[[Category: Dickerson, R E.]]
 [[Category: Grzeskowiak, K.]]
-[[Category: Han, G.W.]]
+[[Category: Han, G W.]]
-[[Category: Kopka, M.L.]]
+[[Category: Kopka, M L.]]
 [[Category: b-dna]]
 [[Category: double helix]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov  8 14:57:48 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:01:52 2008''