Ultraviolet resonance Raman spectra of adenine, uracil and thymine derivatives in several solvents. Correlation between band frequencies and hydrogen-bonding states of the nucleic acid bases

Toyama, Akira; Takeuchi, Hideo; Harada, Issei

doi:10.1016/0022-2860(91)87129-6

Cited by 71 publications

(63 citation statements)

References 16 publications

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“…Carbonyl stretching vibrations typically experience an increase in vibrational frequency with a reduction in H-bonding strength (20). For 1-methylthymine, comparable frequency shifts of the C4dO stretching vibration were observed in a non-H-bond-donating solvent compared to water (24). In the case of the A 3 T 3 duplex, a significant portion of the frequency shift occurs before the duplex melting temperature (∼65°C) has been reached.…”

Section: The 260 Nm-excited Uvrr Spectra (1) Intensity Changesmentioning

confidence: 96%

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UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Mukerji

Williams

2001

Biochemistry

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The presence of A n and A n T n tracts in double-helical sequences perturbs the structural properties of DNA molecules, resulting in the formation of an alternate conformation to standard B-DNA known as B‘-DNA. Evidence for a transition occurring prior to duplex melting in molecules containing A n tracts was previously detected by circular dichroism (CD) and calorimetric studies. This premelting transition was attributed to a conformational change from B‘- to B-DNA. Structural features of A n and A n T n tracts revealed by X-ray crystallography include a large degree of propeller twisting of adenine bases, narrowed minor grooves, and the formation of three-centered H-bonds between dA and dT bases. We report UV resonance Raman (UVRR) and CD spectroscopic studies of two related DNA dodecamer duplexes, d(CGCAAATTTGCG)2 (A3T3) and d(CGCATATATGCG)2 [(AT)3]. These studies address the presence of three-centered H-bonds in the B‘ conformation and gauge the impact of these putative H-bonds on the structural and thermodynamic properties of the A3T3 duplex. UVRR and CD spectra reveal that the premelting transition is only observed for the A3T3 duplex, is primarily localized to the dA and dT bases, and is associated with base stacking interactions. Spectroscopic changes associated with the premelting transition are not readily detectable for the sugar−phosphate backbone or the cytosine and guanosine bases. The temperature-dependent concerted frequency shifts of dA exocyclic NH2 and dT C4O vibrational modes suggest that the A3T3 duplex forms three-centered hydrogen bonds at low temperatures, while the (AT)3 duplex does not. The enthalpy of this H-bond, estimated from the thermally induced frequency shift of the dT C4O vibrational mode, is approximately 1.9 kJ/mol or 0.46 kcal/mol.

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Section: The 260 Nm-excited Uvrr Spectra (1) Intensity Changesmentioning

confidence: 96%

“…e Tm calculated from the nearest neighbor thermodynamic parameters of Santa-Lucia et al (27) at a DNA concentration of 0.1 mM. the C4 carbonyl group (15,24). Carbonyl stretching vibrations typically experience an increase in vibrational frequency with a reduction in H-bonding strength (20).…”

Section: The 260 Nm-excited Uvrr Spectra (1) Intensity Changesmentioning

confidence: 99%

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Mukerji

Williams

2001

Biochemistry

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“…[3][4][5][6][7][8][9] Fourteen different tautomeric species were found, both for the gas-phase and the aqueous solution, 10 comprising four amino and ten imino forms. In fact, adenine's tautomeric equilibrium has been studied in great detail and at different theoretical levels.…”

Section: Introductionmentioning

confidence: 99%

Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

et al. 2013

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A full conformational study of solid-state anhydrous adenine is reported, using vibrational spectroscopy techniques coupled to DFT calculations, for the isolated molecule and the solid. In both cases, the N9H-amino tautomer was found to be the predominant species, followed by the N7H-amino form. An excellent agreement was achieved between experiment and theory, both for wavenumbers and intensities (without the need for scaling). A complete spectral assignment was performed, since all vibrational spectroscopic techniques were available to this study -FTIR, Raman and INS -allowing us to detect and interpret even the lowest frequency vibrational bands, not previously accessed. The quantum mechanical calculations presently carried out represent the highest theoretical level applied so far to the study of nucleobases.

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“…The 1670 cm 1 feature should be assigned to the thymine band, which appeared due to the splitting of the 1652 cm -~ band into 1670/1652 cm 1 doublet [19]. Taken together, this 1670/1652 cm -1 doublet and these 1375, 1250 cm 1 bands correspond to the most intensive bands in the spectrum of dTMP (Fig.…”

Section: The Uv Rr Spectra Of the Ternary Complexesmentioning

confidence: 84%

DNA topoisomerase I changes the mode of interaction between camptothecin drugs and DNA as probed by UV‐resonance Raman spectroscopy

et al. 1996

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Pronounced differences of interactions of camptothecin (CPT) and its derivative 7-ethyl-10-[4-(1-piperidino)-lpiperidino]carbonyloxycamptothecin (CPTll), inhibitors of DNA topoisomerase I, with oligonucleotides were found using UV resonance Raman spectroscopy. 30-mer oligonucleotides were derived from the sequences of the topoisomerase I-induced and CPT-enhanced cleavage sites in SV40 DNA. CPT induces well-defined alterations of the oligo structure, whereas CPTll interacts with oligonucleotides more weakly and in another manner than CPT. Formation of cleavable ternary complexes between CPTll, topoisomerase I and oligonucleotides causes CPTll to interact with oligonucleotides in the same fashion as was found for its parent compound CPT, and enhances this interaction as compared to CPT-oligonucleotide complexes. The data present evidence of molecular interactions of CPTll with both other partners (topoisomerase I and oligonucleotide) of the ternary cleavable complex at the oligonucleotide-enzyme interface.

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Ultraviolet resonance Raman spectra of adenine, uracil and thymine derivatives in several solvents. Correlation between band frequencies and hydrogen-bonding states of the nucleic acid bases

Cited by 71 publications

References 16 publications

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

DNA topoisomerase I changes the mode of interaction between camptothecin drugs and DNA as probed by UV‐resonance Raman spectroscopy

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Ultraviolet resonance Raman spectra of adenine, uracil and thymine derivatives in several solvents. Correlation between band frequencies and hydrogen-bonding states of the nucleic acid bases

Cited by 71 publications

References 16 publications

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A3T3 Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A3T3 Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Applying vibrational spectroscopy to the study of nucleobases – adenine as a case-study

DNA topoisomerase I changes the mode of interaction between camptothecin drugs and DNA as probed by UV‐resonance Raman spectroscopy

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UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds