1s1k: Difference between revisions

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[[Image:1s1k.gif|left|200px]]<br /><applet load="1s1k" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1s1k.gif|left|200px]]<br /><applet load="1s1k" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1s1k, resolution 1.90Å" />

'''INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION'''<br />

==Overview==

The inosine-containing sequence d(CCIGTACm(5)CGG) is shown to crystallize, as a four-stranded DNA junction. This structure is nearly identical to the, antiparallel junction formed by the parent d(CCGGTACm(5)()CGG) sequence, [Vargason, J. M., and Ho, P. S. (2002) J. Biol. Chem. 277, 21041-21049] in, terms of its conformational geometry, and inter- and intramolecular, interactions within the DNA and between the DNA and solvent, even though, the 2-amino group in the minor groove of the important G(3).m(5)C(8) base, pair of the junction core trinucleotide (italicized) has been removed. In, contrast, the analogous 2,6-diaminopurine sequence d(CCDGTACTGG), crystallizes as resolved duplex DNAs, just like its parent sequence, d(CCAGTACTGG) [Hays, F. A., Vargason, J. M., and Ho, P. S. (2003), Biochemistry 42, 9586-9597]. These results demonstrate that it is not the, presence or absence of the 2-amino group in the minor groove of the, R(3).Y(8) base pair that specifies whether a sequence forms a junction, but the positions of the extracyclic amino and keto groups in the major, groove. Finally, the study shows that the arms of the junction can, accommodate perturbations to the B-DNA conformation of the stacked duplex, arms associated with the loss of the 2-amino substituent, and that two, hydrogen bonding interactions from the C(7) and Y(8) pyrimidine, nucleotides to phosphate oxygens of the junction crossover specify the, geometry of the Holliday junction.

The inosine-containing sequence d(CCIGTACm(5)CGG) is shown to crystallize as a four-stranded DNA junction. This structure is nearly identical to the antiparallel junction formed by the parent d(CCGGTACm(5)()CGG) sequence [Vargason, J. M., and Ho, P. S. (2002) J. Biol. Chem. 277, 21041-21049] in terms of its conformational geometry, and inter- and intramolecular interactions within the DNA and between the DNA and solvent, even though the 2-amino group in the minor groove of the important G(3).m(5)C(8) base pair of the junction core trinucleotide (italicized) has been removed. In contrast, the analogous 2,6-diaminopurine sequence d(CCDGTACTGG) crystallizes as resolved duplex DNAs, just like its parent sequence d(CCAGTACTGG) [Hays, F. A., Vargason, J. M., and Ho, P. S. (2003) Biochemistry 42, 9586-9597]. These results demonstrate that it is not the presence or absence of the 2-amino group in the minor groove of the R(3).Y(8) base pair that specifies whether a sequence forms a junction, but the positions of the extracyclic amino and keto groups in the major groove. Finally, the study shows that the arms of the junction can accommodate perturbations to the B-DNA conformation of the stacked duplex arms associated with the loss of the 2-amino substituent, and that two hydrogen bonding interactions from the C(7) and Y(8) pyrimidine nucleotides to phosphate oxygens of the junction crossover specify the geometry of the Holliday junction.

==About this Structure==

1S1K is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CA and NA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1S1K OCA].

1S1K is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1K OCA].

==Reference==

Influence of minor groove substituents on the structure of DNA Holliday junctions., Hays FA, Jones ZJ, Ho PS, Biochemistry. 2004 Aug 3;43(30):9813-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15274635 15274635]

[[Category: Protein complex]]

[[Category: Hays, F.A.]]

[[Category: Hays, F A.]]

[[Category: Ho, P.S.]]

[[Category: Ho, P S.]]

[[Category: Watson, J.]]

[[Category: CA]]

Line 23:

[[Category: minor groove interactions]]

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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:56:53 2008''

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@@ Line 1: / Line 1: @@
-[[Image:1s1k.gif|left|200px]]<br /><applet load="1s1k" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1s1k.gif|left|200px]]<br /><applet load="1s1k" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1s1k, resolution 1.90&Aring;" />
 '''INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION'''<br />
 ==Overview==
-The inosine-containing sequence d(CCIGTACm(5)CGG) is shown to crystallize, as a four-stranded DNA junction. This structure is nearly identical to the, antiparallel junction formed by the parent d(CCGGTACm(5)()CGG) sequence, [Vargason, J. M., and Ho, P. S. (2002) J. Biol. Chem. 277, 21041-21049] in, terms of its conformational geometry, and inter- and intramolecular, interactions within the DNA and between the DNA and solvent, even though, the 2-amino group in the minor groove of the important G(3).m(5)C(8) base, pair of the junction core trinucleotide (italicized) has been removed. In, contrast, the analogous 2,6-diaminopurine sequence d(CCDGTACTGG), crystallizes as resolved duplex DNAs, just like its parent sequence, d(CCAGTACTGG) [Hays, F. A., Vargason, J. M., and Ho, P. S. (2003), Biochemistry 42, 9586-9597]. These results demonstrate that it is not the, presence or absence of the 2-amino group in the minor groove of the, R(3).Y(8) base pair that specifies whether a sequence forms a junction, but the positions of the extracyclic amino and keto groups in the major, groove. Finally, the study shows that the arms of the junction can, accommodate perturbations to the B-DNA conformation of the stacked duplex, arms associated with the loss of the 2-amino substituent, and that two, hydrogen bonding interactions from the C(7) and Y(8) pyrimidine, nucleotides to phosphate oxygens of the junction crossover specify the, geometry of the Holliday junction.
+The inosine-containing sequence d(CCIGTACm(5)CGG) is shown to crystallize as a four-stranded DNA junction. This structure is nearly identical to the antiparallel junction formed by the parent d(CCGGTACm(5)()CGG) sequence [Vargason, J. M., and Ho, P. S. (2002) J. Biol. Chem. 277, 21041-21049] in terms of its conformational geometry, and inter- and intramolecular interactions within the DNA and between the DNA and solvent, even though the 2-amino group in the minor groove of the important G(3).m(5)C(8) base pair of the junction core trinucleotide (italicized) has been removed. In contrast, the analogous 2,6-diaminopurine sequence d(CCDGTACTGG) crystallizes as resolved duplex DNAs, just like its parent sequence d(CCAGTACTGG) [Hays, F. A., Vargason, J. M., and Ho, P. S. (2003) Biochemistry 42, 9586-9597]. These results demonstrate that it is not the presence or absence of the 2-amino group in the minor groove of the R(3).Y(8) base pair that specifies whether a sequence forms a junction, but the positions of the extracyclic amino and keto groups in the major groove. Finally, the study shows that the arms of the junction can accommodate perturbations to the B-DNA conformation of the stacked duplex arms associated with the loss of the 2-amino substituent, and that two hydrogen bonding interactions from the C(7) and Y(8) pyrimidine nucleotides to phosphate oxygens of the junction crossover specify the geometry of the Holliday junction.
 ==About this Structure==
-S1K is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CA and NA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S1K OCA].
+S1K is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1K OCA].
 ==Reference==
 Influence of minor groove substituents on the structure of DNA Holliday junctions., Hays FA, Jones ZJ, Ho PS, Biochemistry. 2004 Aug 3;43(30):9813-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15274635 15274635]
 [[Category: Protein complex]]
-[[Category: Hays, F.A.]]
+[[Category: Hays, F A.]]
-[[Category: Ho, P.S.]]
+[[Category: Ho, P S.]]
 [[Category: Watson, J.]]
 [[Category: CA]]
@@ Line 23: / Line 23: @@
 [[Category: minor groove interactions]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:41:37 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:56:53 2008''