1s1l: Difference between revisions
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==Influence of Groove Interactions on the Formation of DNA Holliday Junctions== | |||
[[ | <StructureSection load='1s1l' size='340' side='right' caption='[[1s1l]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1s1l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S1L FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1s1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s1l RCSB], [http://www.ebi.ac.uk/pdbsum/1s1l PDBsum]</span></td></tr> | |||
<table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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:15274635<ref>PMID:15274635</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
< | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
== | |||
[[Category: Hays, F A.]] | [[Category: Hays, F A.]] | ||
[[Category: Ho, P S.]] | [[Category: Ho, P S.]] | ||
[[Category: Jones, Z J.]] | [[Category: Jones, Z J.]] | ||
[[Category: Dna]] | |||
[[Category: Dna four-way junction]] | [[Category: Dna four-way junction]] | ||
[[Category: Holliday junction]] | [[Category: Holliday junction]] | ||
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[[Category: Major groove]] | [[Category: Major groove]] | ||
[[Category: Minor groove]] | [[Category: Minor groove]] | ||
Revision as of 09:55, 9 June 2014
Influence of Groove Interactions on the Formation of DNA Holliday JunctionsInfluence of Groove Interactions on the Formation of DNA Holliday Junctions
Structural highlights
Publication Abstract from PubMedThe 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. 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:15274635[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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