1H NMR study of self-association of actinomycin D in an aqueous solution

Veselkov, A. N.; Dymant, L. N.; Baranovskii, S. F.; Bolotin, P. A.; Zav'yalova, O. S.; Veselkov, D. A.; Parkes, Harold G.; Davies, David B.

doi:10.1007/bf02577751

Cited by 6 publications

(7 citation statements)

References 12 publications

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“…The C 1 and T 2 spin systems were identified from COSY spectra on the basis of 3 J H5−H6 and 4 J CH3-H6 couplings, respectively. The A 4 assignment was based on the chemical shifts of the aromatic signals and was consistent with published values . The X 3 resonances were assigned via a process of elimination.…”

Section: Resultssupporting

confidence: 71%

“…The tetramer 5′-d(C 1 T 2 X 3 A 4 )-3′ modeled the AFB-α-FAPY adduct in the single strand. NMR experiments were conducted at 0.5 mM concentration, to minimize the potential for self-association by the tetramer, for example, as has been reported for 5′-d(CTGA)-3′( 55 ) and 5′-d(CGA)-3′. ( 56 ) Under these conditions, no self-association of the 5′-d(C 1 T 2 X 3 A 4 )-3′ tetramer was observed.…”

Section: Resultsmentioning

confidence: 99%

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Structural Perturbations Induced by the α-Anomer of the Aflatoxin B₁Formamidopyrimidine Adduct in Duplex and Single-Strand DNA

et al. 2009

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The guanine N7 adduct of aflatoxin B1exo-8,9-epoxide hydrolyzes to form the formamidopyrimidine (AFB-FAPY) adduct, which interconverts between α and β anomers. The β anomer is highly mutagenic in Escherichia coli, producing G → T transversions; it thermally stabilizes the DNA duplex. The AFB-α-FAPY adduct blocks replication; it destabilizes the DNA duplex. Herein, the structure of the AFB-α-FAPY adduct has been elucidated in 5′-d(C1T2A3T4X5A6T7T8C9A10)-3′·5′-d(T11G12A13A14T15C16A17T18A19G20)-3′ (X = AFB-α-FAPY) using molecular dynamics calculations restrained by NMR-derived distances and torsion angles. The AFB moiety intercalates on the 5′ face of the pyrimidine moiety at the damaged nucleotide between base pairs T4·A17 and X5·C16, placing the FAPY C5−N5 bond in the Ra axial conformation. Large perturbations of the ε and ζ backbone torsion angles are observed, and the base stacking register of the duplex is perturbed. The deoxyribose orientation shifts to become parallel to the FAPY base and displaced toward the minor groove. Intrastrand stacking between the AFB moiety and the 5′ neighbor thymine remains, but strong interstrand stacking is not observed. A hydrogen bond between the formyl group and the exocyclic amine of the 3′-neighbor adenine stabilizes the E conformation of the formamide moiety. NMR studies reveal a similar 5′-intercalation of the AFB moiety for the AFB-α-FAPY adduct in the tetramer 5′-d(C1T2X3A4)-3′, involving the Ra axial conformation of the FAPY C5−N5 bond and the E conformation of the formamide moiety. Since in duplex DNA the AFB moiety of the AFB-β-FAPY adduct also intercalates on the 5′ side of the pyrimidine moiety at the damaged nucleotide, we conclude that favorable 5′-stacking leads to the Ra conformational preference about the C5−N5 bond; the same conformational preference about this bond is also observed at the nucleoside and base levels. The structural distortions and the less favorable stacking interactions induced by the AFB-α-FAPY adduct explain its lower stability as compared to the AFB-β-FAPY adduct in duplex DNA. In this DNA sequence, hydrogen bonding between the formyl oxygen and the exocyclic amine of the 3′-neighboring adenine stabilizing the E configuration of the formamide moiety is also observed for the AFB-β-FAPY adduct, and suggests that the identity of the 3′-neighbor nucleotide modulates the stability and biological processing of AFB adducts.

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Section: Resultssupporting

confidence: 71%

Section: Resultsmentioning

confidence: 99%

Structural Perturbations Induced by the α-Anomer of the Aflatoxin B₁Formamidopyrimidine Adduct in Duplex and Single-Strand DNA

et al. 2009

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“…This approach has been used in numerous studies. [35][36][37][38][39][40][41][42][43][44] Most of the previous studies show a decrease in the 1 H chemical shifts with concentration increase, suggesting that the analysed compounds are involved in self-association processes. Upon self-association, 1 H chemical shifts are displaced to lower field due to proton deshieldingthe bond of the proton involved in self-association weakens, bond length increases, stretching frequency decreases.…”

Section: Spectroscopic Self-association Studiesmentioning

confidence: 95%

The reluctant polymorph: investigation into the effect of self-association on the solvent mediated phase transformation and nucleation of theophylline

2015

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“…As a result of these features ethidium has been widely used as a common fluorescence stain and a lot of experimental data on ethidium have been collected over the last three decades. [21][22][23][24][25][29][30][31][32][33] It has been shown experimentally [12] that the intercalation rate of ethidium to DNA is controlled by the insertion of an aromatic ring into the DNA structure. (Earlier, it was suggested that the process was controlled by the diffusion of ethidium toward the DNA.)…”

Section: Introductionmentioning

confidence: 99%

Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations

Kubař

Hanus

Ryjáček

et al. 2005

Chemistry A European J

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Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5-ethyl-6-phenylphenanthridinium and uncharged 3,8-diamino-6-phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge-transfer terms are also important. The DeltaG of ethidium intercalation to DNA was estimated at -4.5 kcal mol(-1) and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non-covalent stacking (including charge-transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.

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1H NMR study of self-association of actinomycin D in an aqueous solution

Cited by 6 publications

References 12 publications

Structural Perturbations Induced by the α-Anomer of the Aflatoxin B₁Formamidopyrimidine Adduct in Duplex and Single-Strand DNA

Structural Perturbations Induced by the α-Anomer of the Aflatoxin B₁Formamidopyrimidine Adduct in Duplex and Single-Strand DNA

The reluctant polymorph: investigation into the effect of self-association on the solvent mediated phase transformation and nucleation of theophylline

Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations

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1H NMR study of self-association of actinomycin D in an aqueous solution

Cited by 6 publications

References 12 publications

Structural Perturbations Induced by the α-Anomer of the Aflatoxin B1Formamidopyrimidine Adduct in Duplex and Single-Strand DNA

Structural Perturbations Induced by the α-Anomer of the Aflatoxin B1Formamidopyrimidine Adduct in Duplex and Single-Strand DNA

The reluctant polymorph: investigation into the effect of self-association on the solvent mediated phase transformation and nucleation of theophylline

Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations

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Structural Perturbations Induced by the α-Anomer of the Aflatoxin B₁Formamidopyrimidine Adduct in Duplex and Single-Strand DNA

Structural Perturbations Induced by the α-Anomer of the Aflatoxin B₁Formamidopyrimidine Adduct in Duplex and Single-Strand DNA