1d81

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[[Image:1d81.gif|left|200px]]
[[Image:1d81.gif|left|200px]]
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{{Structure
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|PDB= 1d81 |SIZE=350|CAPTION= <scene name='initialview01'>1d81</scene>, resolution 2.500&Aring;
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The line below this paragraph, containing "STRUCTURE_1d81", creates the "Structure Box" on the page.
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|SITE=
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DI:2&#39;-DEOXYINOSINE-5&#39;-MONOPHOSPHATE'>DI</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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|DOMAIN=
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{{STRUCTURE_1d81| PDB=1d81 | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d81 OCA], [http://www.ebi.ac.uk/pdbsum/1d81 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d81 RCSB]</span>
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'''THE CONFORMATIONAL VARIABILITY OF AN ADENOSINE. INOSINE BASE-PAIR IN A SYNTHETIC DNA DODECAMER'''
'''THE CONFORMATIONAL VARIABILITY OF AN ADENOSINE. INOSINE BASE-PAIR IN A SYNTHETIC DNA DODECAMER'''
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==About this Structure==
==About this Structure==
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1D81 is a [[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=1D81 OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D81 OCA].
==Reference==
==Reference==
The conformational variability of an adenosine.inosine base-pair in a synthetic DNA dodecamer., Leonard GA, Booth ED, Hunter WN, Brown T, Nucleic Acids Res. 1992 Sep 25;20(18):4753-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1408788 1408788]
The conformational variability of an adenosine.inosine base-pair in a synthetic DNA dodecamer., Leonard GA, Booth ED, Hunter WN, Brown T, Nucleic Acids Res. 1992 Sep 25;20(18):4753-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1408788 1408788]
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[[Category: Protein complex]]
 
[[Category: Booth, E D.]]
[[Category: Booth, E D.]]
[[Category: Brown, T.]]
[[Category: Brown, T.]]
[[Category: Hunter, W N.]]
[[Category: Hunter, W N.]]
[[Category: Leonard, G A.]]
[[Category: Leonard, G A.]]
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[[Category: b-dna]]
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[[Category: B-dna]]
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[[Category: double helix]]
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[[Category: Double helix]]
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[[Category: mismatched]]
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[[Category: Mismatched]]
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[[Category: modified]]
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[[Category: Modified]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:33:16 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:36:26 2008''
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Revision as of 10:33, 2 May 2008

Image:1d81.gif

Template:STRUCTURE 1d81

THE CONFORMATIONAL VARIABILITY OF AN ADENOSINE. INOSINE BASE-PAIR IN A SYNTHETIC DNA DODECAMER


Overview

A crystal structure analysis of the synthetic deoxydodecamer d(CGCAAATTIGCG) which contains two adenosine.inosine (A.I) mispairs has revealed that, in this sequence, the A.I base-pairs adopt a A(anti).I(syn) configuration. The refinement converged at R = 0.158 for 2004 reflections with F greater than or equal to 2 sigma(F) in the range 7.0-2.5A for a model consisting of the DNA duplex and 71 water molecules. A notable feature of the structure is the presence of an almost complete spine of hydration spanning the minor groove of the whole of the (AAATTI)2 core region of the duplex. pH-dependent ultraviolet melting studies have suggested that the base-pair observed in the crystal structure is, in fact, a protonated AH+ (anti).I(syn) species and that the A.I base-pairs in the sequence studied display the same conformational variability as A.G mispairs in the sequence d(CGCAAATTGGCG). The AH+(anti).I(syn) base-pair predominates below pH 6.5 and an A(anti).I(anti) mispair is the major species present between pH 6.5 and 8.0. The protonated base-pairs are held together by two hydrogen bonds one between N6(A) and O6(I) and the other between N1(A) and N7(I). This second hydrogen bond is a direct result of the protonation of the N1 of adenosine. The ultraviolet melting studies indicate that the A(anti).I(anti) base-pair is more stable than the A(anti).G(anti) base-pair but that the AH+(anti).I(syn) base pair is less stable than its AH+(anti).G(syn) analogue. Possible reasons for this observation are discussed.

About this Structure

Full crystallographic information is available from OCA.

Reference

The conformational variability of an adenosine.inosine base-pair in a synthetic DNA dodecamer., Leonard GA, Booth ED, Hunter WN, Brown T, Nucleic Acids Res. 1992 Sep 25;20(18):4753-9. PMID:1408788 Page seeded by OCA on Fri May 2 13:33:16 2008

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