Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6-Diaminide-2-phenylindole) and DNA Base Pairs. <i>Ab Initio</i> Quantum Chemical, Density Functional Theory, and Empirical Potential Study

Rooney, David; Kabeláč, Martin; Ryjáček, Filip; Šponer, Jiřı́; Šponer, Judit E.; Elstner, Marcus; Suhai, Sándor; Hobza, Pavel

doi:10.1021/ja011490d

Cited by 296 publications

(223 citation statements)

References 36 publications

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“…1), which are polycyclic aromatic compounds with a heterocyclic nitrogen atom, are a useful molecules because of their potential as chemotherapeutic agents 2,18 and probes in molecular biology. 19 These molecules are known as intercalators and interact with double stranded DNA and RNA via intercalation. [20][21][22][23][24] Our aim is to scrutinize the thermodynamic stability of 9AA and PF intercalated in DNA base pairs.…”

Section: -13mentioning

confidence: 99%

Effect of Number and Location of Amine Groups on the Thermodynamic Parameters on the Acridine Derivatives to DNA

Kwon¹,

Park²,

Chitrapriya³

et al. 2013

Bulletin of the Korean Chemical Society

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The thermodynamic parameters for the intercalative interaction of structurally related well known intercalators, 9-aminoacridine (9AA) and proflavine (PF) were determined by means of fluorescence quenching study. The fluorescence intensity of 9AA decreased upon intercalation to DNA, poly[d(A-T) 2 ] and poly[d(G-C) 2 ]. A van't Hoff plot was constructed from the temperature-dependence of slope of the ratio of the fluorophore in the absence and presence of a quencher molecule with respect to the quencher concentration, which is known as a Stern-Volmer plot. Consequently, the thermodynamic parameters, enthalpy and entropy change, for complex formation was calculated from the slope and y-intercept of the van't Hoff plot. The detailed thermodynamic profile has been elucidated the exothermic nature of complex formation. The complex formation of 9AA with DNA, poly[d(A-T) 2 ] and poly[d(G-C) 2 ] was energetically favorable with a similar negative Gibb's free energy. On the other hand, the entropy change appeared to be unfavorable for 9AA-poly[d(G-C) 2 ] complex formation, which was in contrast to that observed with native DNA and poly[d(A-T) 2 ] cases. The equilibrium constant for the intercalation of PF to poly[d(G-C) 2 ] was larger than that to DNA, and was the largest among sets tested despite the most unfavorable entropy change, which was compensated for by the largest favorable enthalpy. The favorable hydrogen bond contribution to the formation of the complexes was revealed from the analyzed thermodynamic data.

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Section: -13mentioning

confidence: 99%

Effect of Number and Location of Amine Groups on the Thermodynamic Parameters on the Acridine Derivatives to DNA

Kwon¹,

Park²,

Chitrapriya³

et al. 2013

Bulletin of the Korean Chemical Society

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“…It must nonetheless be noted that electron-transfer from the excited ligand to the DNA is unlikely: the ligands are positively charged, and ligands like ethidium are actually known to be better electron acceptors in their excited-state than in their ground state [47]. The hypothesis of electron-transfer from the DNA to the excited chromophore might be considered given the huge amount of literature about chargetransfer in DNA where hole injection is controlled by chromophores stacked between the DNA bases [48].…”

Section: Mechanism Of Electron Photodetachment Following Chromophore mentioning

confidence: 99%

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

Gabelica

Rosu

Pauw

et al. 2007

J. Am. Soc. Mass Spectrom.

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Double stranded DNA multiply charged anions coupled to chromophores were subjected to UV-Vis photoactivation in a quadrupole ion trap mass spectrometer. The chromophores included noncovalently bound minor groove binders (activated in the near UV), noncovalently bound intercalators (activated with visible light), and covalently linked fluorophores and quenchers (activated at their maximum absorption wavelength). We found that the activation of only chromophores having long fluorescence lifetimes did result in efficient electron photodetachment from the DNA complexes. In the case of ethidium-dsDNA complex excited at 500 nm, photodetachment is a multiphoton process. The MS 3 fragmentation of radicals produced by photodetachment at ϭ 260 nm (DNA excitation) and by photodetachment at Ͼ 300 nm (chromophore excitation) were compared. The radicals keep no memory of the way they were produced. A weakly bound noncovalent ligand (m-amsacrine) allowed probing experimentally that a fraction of the electronic internal energy was converted into vibrational internal energy. This fragmentation channel was used to demonstrate that excitation of the quencher DABSYL resulted in internal conversion, unlike the fluorophore 6-FAM. Altogether, photodetachment of the DNA complexes upon chromophore excitation can be interpreted by the following mechanism: (1) ligands with sufficiently long excited-state lifetime undergo resonant two-photon excitation to reach the level of the DNA excited states, then (2) the excited-state must be coupled to the DNA excited states for photodetachment to occur. Our experiments also pave the way towards photodissociation probes of biomolecule conformation in the gas-phase by Since then, some major advances must be mentioned in electron activation methods [3][4][5] and in infrared photodissociation [6].We recently started exploring the gas-phase reaction pathways of multiply charged DNA single strands and double strands upon UV irradiation around 260 nm [7,8]. To our surprise, we found out that, instead of fragmentation, electron detachment was the major reaction pathway with strands containing guanines. Electron photodetachment itself is not useful for DNA structure analysis, but subsequent collisional activation of the oligonucleotide radicals produced by electron photodetachment gives fragmentation into w, d, a· and z· ions with good sequence coverage [7]. This technique combining electron photodetachment and collision-induced dissociation was coined electron photodetachment dissociation (EPD). It has now been shown to apply to peptides and proteins as well [9].Apart from the sequencing applications of EPD, numerous questions remain about the electron photodetachment mechanism, and how it compares with electron detachment dissociation [3][4][5] and thermal electron detachment [10,11]. We will briefly summarize our current understanding of the photodetachment mechanism [8]. The electron binding energy in multiply charged DNA anions depends on the balance between electron binding energy of the different DNA...

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“…Calculations performed with the second-order Møller-Plesset method using medium-sized AO basis set containing diffuse polarization functions provided meaningful results for base pairing, 30 stacking, 31 for interactions of DNA bases and base pairs with metal cations 32,33 as well as for interactions of DNA base pairs with drugs. 34,35 With the advent of fast and reliable quantum chemical methods, such as RI-DFT-D (resolution of identity density functional theory augmented with dispersion term), 36,37 the size of the system can be considerably increased, representing thus a major progress in ab initio description of nucleic acid systems.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Svozil¹,

Hobza²,

Šponer³

2010

J. Phys. Chem. B

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High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal · mol, which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the CG/CG step that is well separated from the second most stable step GC/GC. Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal · mol -1 per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of ∆G°3 7 free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.

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Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study

Cited by 296 publications

References 36 publications

Effect of Number and Location of Amine Groups on the Thermodynamic Parameters on the Acridine Derivatives to DNA

Effect of Number and Location of Amine Groups on the Thermodynamic Parameters on the Acridine Derivatives to DNA

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

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