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==The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation==
==The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation==
<StructureSection load='1jb8' size='340' side='right' caption='[[1jb8]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
<StructureSection load='1jb8' size='340' side='right'caption='[[1jb8]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1jb8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JB8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1jb8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JB8 FirstGlance]. <br>
</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=1jb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jb8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jb8 RCSB], [http://www.ebi.ac.uk/pdbsum/1jb8 PDBsum]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38&#8491;</td></tr>
<table>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jb8 OCA], [https://pdbe.org/1jb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jb8 RCSB], [https://www.ebi.ac.uk/pdbsum/1jb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jb8 ProSAT]</span></td></tr>
<div style="background-color:#fffaf0;">
</table>
== Publication Abstract from PubMed ==
An intermolecular intercalation of base pairs was found at the CA step in the I222 crystal structure of the RNA.DNA hybrid, r(CAAAGAAAAG).d(CTTTTCTTTG), which contains two-thirds of the polypurine tract sequence of HIV-1 with a substitution of cytosine for the initial adenine. This sequence crystallized in both P212121 and I222 space groups, with an rms difference of only 0.63 A between residues 3 to 18 of the two forms. P212121 and I222 helices are both A-like, but intercalation occurs only in the I222 crystal form. The present structure shows bases stacked in parallel rather than perpendicular as in intercalated DNA (I-DNA). The base intercalation is also different from zipper-like meshing of bases seen in the center of the crystal structure of d(GCGAAAGCT), which does not have Watson-Crick base pairing. The base-step intercalation seen here is reminiscent of domain swapping in proteins; therefore, we call this phenomenon "base-pair swapping." It involves a highly mobile CA step and seems to be sequence-specific and electrostatically stable without disrupting Watson-Crick interactions. It also exhibits a large rise concurrent with unwinding of the helix (low twist). We present a base-pair swapping dimer in nucleic acids.
 
Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping.,Han GW, Kopka ML, Langs D, Sawaya MR, Dickerson RE Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9214-9. Epub 2003 Jul 18. PMID:12872000<ref>PMID:12872000</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Dickerson, R E.]]
[[Category: Large Structures]]
[[Category: Han, G W.]]
[[Category: Dickerson RE]]
[[Category: Kopka, M L.]]
[[Category: Han GW]]
[[Category: Langs, D.]]
[[Category: Kopka ML]]
[[Category: Dna-rna complex]]
[[Category: Langs D]]
[[Category: Dna/dna intercalation]]
[[Category: Rna/dna hybrid]]
[[Category: Rna/dna polypurine tract]]

Latest revision as of 10:38, 7 February 2024

The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular IntercalationThe Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation

Structural highlights

1jb8 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.38Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1jb8, resolution 2.38Å

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