| Base pair recognition of the stereochemically alpha-substituted gamma-turn of pyrrole/imidazole hairpin polyamides. | |
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MedLine Citation:
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PMID: 17105301 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Recognition of the sequences 5'-NGCACA-3' (N = T, A, C, G) by pyrrole/imidazole polyamides with (R/S)-alpha-hydroxyl/alpha-amino-substituted gamma-aminobutyric acid as a gamma-turn was investigated. Four novel polyamides, 2, 3, 4, and 5, including (R)-alpha-hydroxyl-gamma-aminobutyric acid (gammaRO), (S)-alpha-hydroxyl-gamma-aminobutyric acid (gammaSO), (R)-alpha,gamma-diaminobutyric acid (gammaRN), and (S)-alpha,gamma-diaminobutyric acid (gammaSN) residues, respectively, were synthesized, and their binding affinity to T.A, A.T, G.C, and C.G base pairs at turn position was studied by the surface plasmon resonance (SPR) technique. SPR data revealed that polyamide 3, AcImbetaImPy-gammaSO-ImPybetaPy-beta-Dp, with a gammaSO turn, possesses a marked binding preference for T.A over A.T with a 25-fold increase in specificity, despite low binding affinity relative to 2, with a gammaRO turn. Similarly, AcImbetaImPy-gammaSN-ImPybetaPy-beta-Dp (5), with a gammaSN-turn, gives rise to a 8.7-fold increase in specificity for T.A over A.T. Computer-assisted molecular modeling suggests that 3 binds more deeply in the minor groove of the T.A base pair relative to the A.T base pair, allowing hydrogen bonding to O2 of the thymine at the turn position, which explains the SPR results. These results suggest that gammaSO and gammaSN may function as T-recognition units at the turn position, as well as a gamma-turn in the discrimination of polyamides. |
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Authors:
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Wen Zhang; Masafumi Minoshima; Hiroshi Sugiyama |
Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Journal of the American Chemical Society Volume: 128 ISSN: 0002-7863 ISO Abbreviation: J. Am. Chem. Soc. Publication Date: 2006 Nov |
Date Detail:
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Created Date: 2006-11-19 Completed Date: 2007-09-05 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 7503056 Medline TA: J Am Chem Soc Country: United States |
Other Details:
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Languages: eng Pagination: 14905-12 Citation Subset: IM |
Affiliation:
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Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Base Pairing* Base Sequence Imidazoles / chemistry* Models, Molecular Nylons / chemistry* Pyrroles / chemistry* Stereoisomerism Surface Plasmon Resonance |
| Chemical | |
Reg. No./Substance:
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0/Imidazoles; 0/Nylons; 0/Pyrroles |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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