2dqq
From Proteopedia
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| - | [[Image:2dqq.gif|left|200px]] | + | [[Image:2dqq.gif|left|200px]] |
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| - | '''Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine''' | + | {{Structure |
| + | |PDB= 2dqq |SIZE=350|CAPTION= <scene name='initialview01'>2dqq</scene>, resolution 2.0Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=CMY:(6-AMINOHEXYL)CARBAMIC ACID'>CMY</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2DQQ is a [ | + | 2DQQ 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=2DQQ OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules., Juan EC, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takenaka A, Nucleic Acids Res. 2007;35(6):1969-77. Epub 2007 Mar 6. PMID:[http:// | + | Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules., Juan EC, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takenaka A, Nucleic Acids Res. 2007;35(6):1969-77. Epub 2007 Mar 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17341465 17341465] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Ito, T.]] | [[Category: Ito, T.]] | ||
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[[Category: modified nucleotide]] | [[Category: modified nucleotide]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:30:17 2008'' |
Revision as of 14:30, 20 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine
Overview
Oligonucleotides containing 5-(N-aminohexyl)carbamoyl-modified uracils have promising features for applications as antigene and antisense therapies. Relative to unmodified DNA, oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine ((N)U) or 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine ((N)U(m)), respectively exhibit increased binding affinity for DNA and RNA, and enhanced nuclease resistance. To understand the structural implications of (N)U and (N)U(m) substitutions, we have determined the X-ray crystal structures of DNA:DNA duplexes containing either (N)U or (N)U(m) and of DNA:RNA hybrid duplexes containing (N)U(m). The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal ammonium cations on these chains could interact with the phosphate oxygen anions of the residues in the target strands. These interactions partly account for the increased target binding affinity and nuclease resistance. In contrast to (N)U, (N)U(m) decreases DNA binding affinity. This could be explained by the drastic changes in sugar puckering and in the minor groove widths and hydration structures seen in the (N)U(m) containing DNA:DNA duplex structure. The conformation of (N)U(m), however, is compatible with the preferred conformation in DNA:RNA hybrid duplexes. Furthermore, the ability of (N)U(m) to render the duplexes with altered minor grooves may increase nuclease resistance and elicit RNase H activity.
About this Structure
2DQQ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules., Juan EC, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takenaka A, Nucleic Acids Res. 2007;35(6):1969-77. Epub 2007 Mar 6. PMID:17341465
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