Electrostatic effects on the rates of DNA-catalyzed reactions

Pack, George R.; Wong, Linda

doi:10.1016/0301-0104(95)00296-0

Cited by 11 publications

(6 citation statements)

References 35 publications

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“…It has been observed that the luminescence is restored upon interaction with some polynucleotides , , which makes this unit less reducing, and (ii) unfolding of the molecule as also observed by Schanze et al …”

Section: Discussionmentioning

confidence: 53%

“…It has been observed that the luminescence is restored upon interaction with some polynucleotides. 58 Indeed the polynucleotide induces (i) protonation of the quinoline moiety 59,60 , which makes this unit less reducing, and (ii) unfolding of the molecule as also observed by Schanze et al 61 for other complexes. To increase the efficiency of the Ru(II) bifunctional complex as a DNA photoprobe, the intramolecular luminescence quenching in water should be further increased.…”

Section: Discussionmentioning

confidence: 59%

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Photophysics of Bifunctional Ru(II) Complexes Bearing an Aminoquinoline Organic Unit. Potential New Photoprobes and Photoreagents of DNA

and¹,

Mesmaeker²,

and³

et al. 1997

J. Phys. Chem. B

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[Ru(BPY)2POQ−Nmet]2+ and [Ru(TAP)2POQ−Nmet]2+ (1 and 3) are bifunctional complexes composed of a metallic unit linked by a flexible chain to an organic unit. They have been prepared as photoprobes or photoreagents of DNA. In this work, the spectroscopic properties of these bifunctional complexes in the absence of DNA are compared with those of the monofunctional analogues [Ru(BPY)2Phen]2+, [Ru(BPY)2acPhen]2+, [Ru(TAP)2Phen]2+, and [Ru(TAP)2acPhen]2+ (2 and 4). The electrospray mass spectrometry and absorption data show that the quinoline moiety exists in the protonated and nonprotonated form. Although the bifunctional complex containing 2,2‘-bipyridine (BPY) ligands exhibits photophysical properties similar to those of the monofunctional compounds, the bifunctional complex with 1,4,5,8-tetraazaphenanthrene (TAP) ligands behaves quite differently. It has weaker relative emission quantum yields and shorter luminescence lifetimes than the monofunctional TAP analogue when the quinoline unit is nonprotonated. This indicates an efficient intramolecular quenching of the 3MLCT (metal to ligand charge transfer) excited state of the TAP metallic moiety. When the organic unit is protonated, there is no internal quenching. In organic solvent, the nonquenched excited metallic unit (bearing a protonated quinoline) and the quenched one (bearing a nonprotonated organic unit) are in slow equilibrium as compared to the lifetime of the two emitters. In aqueous solution this equilibrium is faster and is catalysed by the presence of phosphate buffer. Flash photolysis experiments suggest that the intramolecular quenching process originates from a photoinduced electron transfer from the nonprotonated quinoline to the excited Ru(TAP)2 2+ moiety.

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Section: Discussionmentioning

confidence: 53%

Section: Discussionmentioning

confidence: 59%

Photophysics of Bifunctional Ru(II) Complexes Bearing an Aminoquinoline Organic Unit. Potential New Photoprobes and Photoreagents of DNA

and¹,

Mesmaeker²,

and³

et al. 1997

J. Phys. Chem. B

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“…pH 4, thus simplifies the interpretation of the kinetics data by restricting the reaction to the direct reaction of the aqua complex with the target group on the DNA. In addition, it minimizes the kinetics influence from a possible pH gradient which may arise due to a higher concentration of oxonium ions on the oligonucleotide surface compared that of the bulk solution [49,50,51] (vide infra). The observed reactivity for the corresponding reactions at pH 7 can be estimated to be at least one order of magnitude lower compared to the ones determined in the present study [7].…”

Section: Oligonucleotidesmentioning

confidence: 99%

Kinetics and mechanism for platination of thione-containing nucleotides and oligonucleotides: evaluation of the salt dependence

Kjellström

Elmroth

2003

J Biol Inorg Chem

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Reactions of cis-[PtCl(NH(3))(CyNH(2))(OH(2))](+) (Cy=cyclohexyl) with thione-containing single-stranded oligonucleotides d(T(8)XT(8)) and d(XT(16)) (X=(s6)I or (s4)U) and the mononucleotides 4-thiouridine ((s4)UMP) and 6-mercaptoinosine ((s6)IMP) have been studied in aqueous solution at pH 4.1. The reaction kinetics was followed using HPLC methodology as a function of ionic strength in the interval 5.0 mM

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“…The activity coefficient for an ion depends on the electrostatic potential; near a polyelectrolyte such as DNA the spatially varying electrostatic potential results in activity coefficients that can be mapped throughout space using electrostatic potentials calculated in the continuum Poisson-Boltzmann approximation (Pack and Wong, 1996;Lamm et al, 1996). The potentials external to the macroion are relatively insensitive to the choice of dielectric constant of the DNA and so can be used to provide an approximate computational scheme for the estimation of the proton equilibria at the DNA surface.…”

Section: Calculation Of Adduct Conformationsmentioning

confidence: 99%

Proton equilibria in the minor groove of DNA

Hanlon¹,

Wong²,

Pack³

1997

Biophysical Journal

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Poisson-Boltzmann calculations by Pack and co-workers suggest the presence of regions of increased hydrogen ion density in the grooves of DNA. As an experimental test of this prediction, we have attached proton-sensitive probes, with variable linker lengths, to random-sequence DNA at G sites in the minor groove. The amino groups of beta-alanine, gamma-aminobutyric acid (GABA), and epsilon-aminocaproic acid have been coupled at pH 5, via a formaldehyde link, to the exocyclic amino group of guanine, utilizing a reaction that has been extensively investigated by Hanlon and co-workers. The resulting adducts at pH 5 retained duplex B form but exhibited typical circular dichroism (CD) changes previously shown to be correlated with the presence of a net positive charge in the minor groove. Increases in the solvent pH reversed the CD spectral changes in a manner suggesting deprotonation of the carboxylic acid group of the adduct. These data were used to calculate an apparent pK(a) for the COOH. The pK(a) was increased by 2.4 units for beta-alanine, by 1.7 units for GABA, and by 1.5 units for epsilon-amino caproic acid, relative to their values in the free amino acid. This agrees well with Poisson-Boltzmann calculations and the energy minimization of the structures of the adducts that place the carboxyl groups in acidic domains whose hydrogen ion density is approximately 2 orders of magnitude greater than that of bulk solvent.

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Electrostatic effects on the rates of DNA-catalyzed reactions

Cited by 11 publications

References 35 publications

Photophysics of Bifunctional Ru(II) Complexes Bearing an Aminoquinoline Organic Unit. Potential New Photoprobes and Photoreagents of DNA

Photophysics of Bifunctional Ru(II) Complexes Bearing an Aminoquinoline Organic Unit. Potential New Photoprobes and Photoreagents of DNA

Kinetics and mechanism for platination of thione-containing nucleotides and oligonucleotides: evaluation of the salt dependence

Proton equilibria in the minor groove of DNA

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