| Quantitative analysis of DNA-porphyrin interactions. | |
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MedLine Citation:
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PMID: 16358258 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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The binding of manganese(III)-tetra(4-N-methylpyridyl)porphyrin (MnTMpyP) with synthetic poly(dA-dT)2, poly(dI-dC)2, and poly(dG-dC)2 DNAs as well as calf thymus (CT) DNA has been quantitatively studied in detail using induced CD (circular dichroism) spectroscopy in the Soret absorption band. The CD spectra, which changed greatly depending on the porphyrin to DNA base-pair molar ratio (r), were normalized with respect to DNA concentration and deconvoluted. Three independent component binding modes (named mode 1, 2, and 3 in the order of increasing r values) were identified, which successfully simulated the observed CD spectra with negligibly small residuals for a wide range of r values. In the case of poly(dA-dT)2, poly (dI-dC)2, and CT DNA, all the three modes appeared, whereas in the case of poly(dG-dC)2 DNA, only modes 1 and 3 appeared in the r range studied. The r dependence of each binding mode, i.e., its relative affinity toward DNA, has been revealed by this analysis. Mode 1, which appeared as a single binding mode at very low r values (r < or = ca. 0.05), was inhibited by the addition of methyl green, a drug that preferentially binds to the major groove of poly (dA-dT)2 DNA. Berenil, a known minor groove binder to poly(dA-dT)2 or poly(dI-dC)2 DNA, inhibited modes 2 and 3. From these inhibition experiments as well as comparison of the component spectra for DNAs of different sequence, a binding site on DNA was proposed for each component binding mode. The number of DNA base pairs covered by a single molecule of porphyrin was estimated. |
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Authors:
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Y Nitta; R Kuroda |
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Publication Detail:
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Type: Journal Article |
Journal Detail:
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Title: Biopolymers Volume: 81 ISSN: 0006-3525 ISO Abbreviation: Biopolymers Publication Date: 2006 Apr |
Date Detail:
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Created Date: 2006-02-28 Completed Date: 2006-06-23 Revised Date: 2008-11-21 |
Medline Journal Info:
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Nlm Unique ID: 0372525 Medline TA: Biopolymers Country: United States |
Other Details:
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Languages: eng Pagination: 376-91 Citation Subset: IM |
Copyright Information:
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Copyright 2005 Wiley Periodicals, Inc. |
Affiliation:
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Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902 Japan. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Biopolymers
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chemistry* Circular Dichroism DNA / chemistry* Diminazene / analogs & derivatives, chemistry Ligands Methyl Green / chemistry Models, Chemical Models, Statistical Nucleic Acid Conformation Nucleic Acid Denaturation Oligodeoxyribonucleotides Polydeoxyribonucleotides Polynucleotides Porphyrins / chemistry* Protein Binding Protein Conformation Protein Structure, Tertiary Spectrophotometry Static Electricity Temperature |
| Chemical | |
Reg. No./Substance:
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0/Biopolymers; 0/Ligands; 0/Oligodeoxyribonucleotides; 0/Polydeoxyribonucleotides; 0/Polynucleotides; 0/Porphyrins; 536-71-0/Diminazene; 82-94-0/Methyl Green; 9007-49-2/DNA; 908-54-3/diminazene aceturate |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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