1cx5

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[[Image:1cx5.gif|left|200px]]
[[Image:1cx5.gif|left|200px]]
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{{Structure
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|PDB= 1cx5 |SIZE=350|CAPTION= <scene name='initialview01'>1cx5</scene>
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The line below this paragraph, containing "STRUCTURE_1cx5", creates the "Structure Box" on the page.
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|SITE=
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</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=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MMT:5&#39;-O-(DIMETHYLAMINO)-THYMIDINE'>MMT</scene>
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{{STRUCTURE_1cx5| PDB=1cx5 | SCENE= }}
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cx5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cx5 OCA], [http://www.ebi.ac.uk/pdbsum/1cx5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cx5 RCSB]</span>
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'''ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE'''
'''ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE'''
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==About this Structure==
==About this Structure==
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1CX5 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=1CX5 OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CX5 OCA].
==Reference==
==Reference==
NMR structure of an antisense DNA.RNA hybrid duplex containing a 3'-CH(2)N(CH(3))-O-5' or an MMI backbone linker., Yang X, Han X, Cross C, Bare S, Sanghvi Y, Gao X, Biochemistry. 1999 Sep 28;38(39):12586-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10504227 10504227]
NMR structure of an antisense DNA.RNA hybrid duplex containing a 3'-CH(2)N(CH(3))-O-5' or an MMI backbone linker., Yang X, Han X, Cross C, Bare S, Sanghvi Y, Gao X, Biochemistry. 1999 Sep 28;38(39):12586-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10504227 10504227]
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[[Category: Protein complex]]
 
[[Category: Cross, C.]]
[[Category: Cross, C.]]
[[Category: Gao, X.]]
[[Category: Gao, X.]]
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[[Category: Sanghvi, Y.]]
[[Category: Sanghvi, Y.]]
[[Category: Yang, X.]]
[[Category: Yang, X.]]
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[[Category: antisense]]
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[[Category: Antisense]]
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[[Category: dna/rna hybrid]]
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[[Category: Dna/rna hybrid]]
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[[Category: modified backbone linker]]
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[[Category: Modified backbone linker]]
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[[Category: nmr]]
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[[Category: Nmr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:12:38 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:30:16 2008''
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Revision as of 10:12, 2 May 2008

Image:1cx5.gif

Template:STRUCTURE 1cx5

ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE


Overview

The solution structure of an antisense DNA.RNA hybrid duplex, d(CGCGTT-MMI-TTGCGC).r(GCGCAAAACGCG) (designated R4), containing an MMI backbone linker [3'-CH(2)N(CH(3))-O5'], is elucidated. The structural details of the MMI linker, its structural effects on the neighboring residues, and the molecular basis of the MMI effects are examined. The lipophilic N-methyl group of MMI is peripheral to the helix, assuming a conformation that is most stable with regard to the N-O torsion angle. The MMI linker promotes a 3'-endo conformation for the sugar moieties at both 3'- and 5'-adjacent positions and a backbone kink involving distant residues along the 3'-direction. Comparison of R4 with other analogous hybrid duplexes previously studied in this laboratory reveals a new family of low-energy helical conformations that can be accommodated in stable duplexes and a common feature of C3'-modified sugars for adopting a C3'-endo pucker. The results of these studies emphasize the interplay of several factors that govern the formation of stable hybrid duplexes and provide a basis for the understanding of the biological role of the MMI modifications, which are important building blocks for a family of promising chimeric antisense oligonucleotides.

About this Structure

Full crystallographic information is available from OCA.

Reference

NMR structure of an antisense DNA.RNA hybrid duplex containing a 3'-CH(2)N(CH(3))-O-5' or an MMI backbone linker., Yang X, Han X, Cross C, Bare S, Sanghvi Y, Gao X, Biochemistry. 1999 Sep 28;38(39):12586-96. PMID:10504227 Page seeded by OCA on Fri May 2 13:12:38 2008

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