Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling

E. M. Proudfoot, J. P. Mackay, P. Karuso

Research output: Contribution to journalArticleResearchpeer-review

Abstract

The molecular recognition of oligonucleotides by chiral ruthenium complexes has been probed by NMR spectroscopy using the template Δ-cis-α- and Δ-cis-β-[Ru(RR-picchxnMe2) (bidentate)]2+, where the bidentate ligand is one of phen (1,10-phenanthroline), dpq (dipyrido[3,2-f:2′,3′-h]quinoxaline), or phi (9,10-phenanthrenequinone diimine) and picchxnMe2 is N,N′-dimethyl-N,N′-di(2-picolyl)-1,2-diaminocyclohexane. By varying only the bidentate ligand in a series of complexes, it was shown that the bidentate alone can alter binding modes. DNA binding studies of the Δ-cis-α,-[Ru(RR-picchxnMe2)(phen)]2+ complex indicate fast exchange kinetics on the chemical shift time scale and a "partial intercalation" mode of binding. This complex binds to [d(CGCGATCGCG)]2 and [d(ATATCGATAT)]2 at AT, TA, and GA sites from the minor groove, as well as to the ends of the oligonucleotide at low temperature. Studies of the Δ-cis-β-[Ru(RR-picchxnMe2)(phen)]2+ complex with [d(CGCGATCGCG)]2 showed that the complex binds only weakly to the ends of the oligonucleotide. The interaction of Δ-cis-α-[Ru(RR-picchxnMe2)-(dpq)]2+ with [d(CGCGATCGCG)]2 showed intermediate exchange kinetics and evidence of minor groove intercalation at the GA base step. In contrast to the phen and dpq complexes, Δ-cis-α- and Δ-cis-β-[Ru-(RR-picchxnMe2)(phi)]2+ showed evidence of major groove binding independent of the metal ion configuration. DNA stabilization induced by complex binding to [d(CGCGATCGCG)]2 (measured as ΔTm) increases in the order phen < dpq and DNA affinity in the order phen < dpq < phi. The groove binding preferences exhibited by the different bidentate ligands is explained with the aid of molecular modeling experiments.

LanguageEnglish
Pages4867-4878
Number of pages12
JournalBiochemistry
Volume40
Issue number15
DOIs
Publication statusPublished - 17 Apr 2001

Fingerprint

Molecular modeling
Nuclear magnetic resonance spectroscopy
Magnetic Resonance Spectroscopy
Oligonucleotides
DNA
Intercalation
Ligands
Quinoxalines
Molecular recognition
Kinetics
Ruthenium
Chemical shift
Metal ions
Stabilization
Metals
Ions
Temperature
d(CGCGATCGCG)2
Experiments

Cite this

@article{7f693a1c244b475ea7df9233164bc764,
title = "Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling",
abstract = "The molecular recognition of oligonucleotides by chiral ruthenium complexes has been probed by NMR spectroscopy using the template Δ-cis-α- and Δ-cis-β-[Ru(RR-picchxnMe2) (bidentate)]2+, where the bidentate ligand is one of phen (1,10-phenanthroline), dpq (dipyrido[3,2-f:2′,3′-h]quinoxaline), or phi (9,10-phenanthrenequinone diimine) and picchxnMe2 is N,N′-dimethyl-N,N′-di(2-picolyl)-1,2-diaminocyclohexane. By varying only the bidentate ligand in a series of complexes, it was shown that the bidentate alone can alter binding modes. DNA binding studies of the Δ-cis-α,-[Ru(RR-picchxnMe2)(phen)]2+ complex indicate fast exchange kinetics on the chemical shift time scale and a {"}partial intercalation{"} mode of binding. This complex binds to [d(CGCGATCGCG)]2 and [d(ATATCGATAT)]2 at AT, TA, and GA sites from the minor groove, as well as to the ends of the oligonucleotide at low temperature. Studies of the Δ-cis-β-[Ru(RR-picchxnMe2)(phen)]2+ complex with [d(CGCGATCGCG)]2 showed that the complex binds only weakly to the ends of the oligonucleotide. The interaction of Δ-cis-α-[Ru(RR-picchxnMe2)-(dpq)]2+ with [d(CGCGATCGCG)]2 showed intermediate exchange kinetics and evidence of minor groove intercalation at the GA base step. In contrast to the phen and dpq complexes, Δ-cis-α- and Δ-cis-β-[Ru-(RR-picchxnMe2)(phi)]2+ showed evidence of major groove binding independent of the metal ion configuration. DNA stabilization induced by complex binding to [d(CGCGATCGCG)]2 (measured as ΔTm) increases in the order phen < dpq and DNA affinity in the order phen < dpq < phi. The groove binding preferences exhibited by the different bidentate ligands is explained with the aid of molecular modeling experiments.",
author = "Proudfoot, {E. M.} and Mackay, {J. P.} and P. Karuso",
year = "2001",
month = "4",
day = "17",
doi = "10.1021/bi001655f",
language = "English",
volume = "40",
pages = "4867--4878",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "15",

}

Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling. / Proudfoot, E. M.; Mackay, J. P.; Karuso, P.

In: Biochemistry, Vol. 40, No. 15, 17.04.2001, p. 4867-4878.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling

AU - Proudfoot, E. M.

AU - Mackay, J. P.

AU - Karuso, P.

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Y1 - 2001/4/17

N2 - The molecular recognition of oligonucleotides by chiral ruthenium complexes has been probed by NMR spectroscopy using the template Δ-cis-α- and Δ-cis-β-[Ru(RR-picchxnMe2) (bidentate)]2+, where the bidentate ligand is one of phen (1,10-phenanthroline), dpq (dipyrido[3,2-f:2′,3′-h]quinoxaline), or phi (9,10-phenanthrenequinone diimine) and picchxnMe2 is N,N′-dimethyl-N,N′-di(2-picolyl)-1,2-diaminocyclohexane. By varying only the bidentate ligand in a series of complexes, it was shown that the bidentate alone can alter binding modes. DNA binding studies of the Δ-cis-α,-[Ru(RR-picchxnMe2)(phen)]2+ complex indicate fast exchange kinetics on the chemical shift time scale and a "partial intercalation" mode of binding. This complex binds to [d(CGCGATCGCG)]2 and [d(ATATCGATAT)]2 at AT, TA, and GA sites from the minor groove, as well as to the ends of the oligonucleotide at low temperature. Studies of the Δ-cis-β-[Ru(RR-picchxnMe2)(phen)]2+ complex with [d(CGCGATCGCG)]2 showed that the complex binds only weakly to the ends of the oligonucleotide. The interaction of Δ-cis-α-[Ru(RR-picchxnMe2)-(dpq)]2+ with [d(CGCGATCGCG)]2 showed intermediate exchange kinetics and evidence of minor groove intercalation at the GA base step. In contrast to the phen and dpq complexes, Δ-cis-α- and Δ-cis-β-[Ru-(RR-picchxnMe2)(phi)]2+ showed evidence of major groove binding independent of the metal ion configuration. DNA stabilization induced by complex binding to [d(CGCGATCGCG)]2 (measured as ΔTm) increases in the order phen < dpq and DNA affinity in the order phen < dpq < phi. The groove binding preferences exhibited by the different bidentate ligands is explained with the aid of molecular modeling experiments.

AB - The molecular recognition of oligonucleotides by chiral ruthenium complexes has been probed by NMR spectroscopy using the template Δ-cis-α- and Δ-cis-β-[Ru(RR-picchxnMe2) (bidentate)]2+, where the bidentate ligand is one of phen (1,10-phenanthroline), dpq (dipyrido[3,2-f:2′,3′-h]quinoxaline), or phi (9,10-phenanthrenequinone diimine) and picchxnMe2 is N,N′-dimethyl-N,N′-di(2-picolyl)-1,2-diaminocyclohexane. By varying only the bidentate ligand in a series of complexes, it was shown that the bidentate alone can alter binding modes. DNA binding studies of the Δ-cis-α,-[Ru(RR-picchxnMe2)(phen)]2+ complex indicate fast exchange kinetics on the chemical shift time scale and a "partial intercalation" mode of binding. This complex binds to [d(CGCGATCGCG)]2 and [d(ATATCGATAT)]2 at AT, TA, and GA sites from the minor groove, as well as to the ends of the oligonucleotide at low temperature. Studies of the Δ-cis-β-[Ru(RR-picchxnMe2)(phen)]2+ complex with [d(CGCGATCGCG)]2 showed that the complex binds only weakly to the ends of the oligonucleotide. The interaction of Δ-cis-α-[Ru(RR-picchxnMe2)-(dpq)]2+ with [d(CGCGATCGCG)]2 showed intermediate exchange kinetics and evidence of minor groove intercalation at the GA base step. In contrast to the phen and dpq complexes, Δ-cis-α- and Δ-cis-β-[Ru-(RR-picchxnMe2)(phi)]2+ showed evidence of major groove binding independent of the metal ion configuration. DNA stabilization induced by complex binding to [d(CGCGATCGCG)]2 (measured as ΔTm) increases in the order phen < dpq and DNA affinity in the order phen < dpq < phi. The groove binding preferences exhibited by the different bidentate ligands is explained with the aid of molecular modeling experiments.

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U2 - 10.1021/bi001655f

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