Initial Excited-State Structural Dynamics of 9-Methyladenine from UV Resonance Raman Spectroscopy

2014

J. Phys. Chem. A

Self Cite

Substituents on the pyrimidine ring of nucleobases appear to play a major role in determining their initial excited-state structural dynamics and resulting photochemistry. To better understand the determinants of nucleobase initial excited-state structural dynamics, we have measured the absorption and resonance Raman excitation profiles of 6-deuterouracil (6-d-U) and 6-methyluracil (6-MeU). Simulation of the resonance Raman excitation profiles and absorption spectrum with a self-consistent, time-dependent formalism shows the effect of the deuterium and methyl group on the photochemically active internal coordinates, i.e. C5C6 stretch and C5X and C6X bends. The methyl group on either the C5 or C6 position of uracil equally increases the excited-state reorganization energies along the C5C6 stretch. However, a lower reorganization energy of the C5X + C6X bends in 6-MeU than uracil and 5-MeU shows that C6 methyl substituents reduce the bending reorganization energy. In addition, deuterium substitution at either C5 or C6 has a much smaller effect on the initial excited-state structural dynamics than methyl substitution, consistent with a mass effect. These results will be discussed in light of the resulting photochemistry of pyrimidine nucleobases.

“…6,9,11,12 Spectral slit widths were 5−7 cm −1 . Spectral line widths are larger than the slit bandwidth due to broadening by the laser source and subsequent frequency multiplication.…”

Section: ■ Experimental Sectionmentioning

confidence: 99%

Section: ■ Theorymentioning

confidence: 99%

Initial Excited-State Structural Dynamics of 6-Substituted Uracil Derivatives: Femtosecond Angle and Bond Lengthening Dynamics in Pyrimidine Nucleobase Photochemistry

Teimoory

2014

J. Phys. Chem. A

Self Cite

“…The observed decrease in the initial excited‐state dynamics has been attributed to the presence of less‐steep excited‐state potential energy surfaces and a shift in the potential energy surface at the Frank–Condon region in nucleosides . The initial excited‐state structural dynamics of 2′‐deoxyguanosine and 9‐methyladenine were studied and are consistent with their resulting photochemistry for corresponding nucleobases. Adenine and guanosine nucleobases are not as photochemically active as the pyrimidine nucleobases, and the resonance Raman intensities and resulting initial excited‐state structural dynamics of their respective nucleosides are also smaller than those of the pyrimidines, further suggesting a positive correlation between steepness of the potential energy surface and photochemical quantum yield.…”

Section: Introductionmentioning

confidence: 74%

Initial excited‐state structural dynamics of uridine from resonance Raman spectroscopy

Sasidharanpillai

Dempster

2018

J Raman Spectroscopy

Self Cite

The effect of the N1 ribose sugar on the initial excited‐state structural dynamics of uridine is explored with ultraviolet resonance Raman spectroscopy. Excited‐state slopes and broadening parameters were obtained by simulating the resonance Raman excitation profiles and absorption spectrum using a self‐consistent, time‐dependent formalism. The initial excited‐state structural dynamics of uridine look similar to those of uracil, in terms of the distribution of percentage of reorganization energy along different modes, but there is an overall decrease in the excited‐state slopes along most of the modes in uridine compared with uracil. Only about 30% of the total initial reorganization energy in both uracil and uridine are oriented along the photochemically reactive coordinates. The results are also similar to those of thymine and thymidine, upon attachment of the sugar. These differences between thymine, thymidine, uracil and uridine are examined, and the possible effect on the resulting differences in photochemistry is discussed.

“…Thus, there is a possibility of forming various photoproducts. Previous studies have shown that UVC irradiation of DNA strands containing “AATTAA” would produce the AA and TA photoproducts, along with the CPD and [6‐4] PP. However, the AA and TA photochemical yields are at most only 10% of those of TT, making these products much less probable .…”

Section: Resultsmentioning

confidence: 99%

Multiplexed, UVC‐Induced, Sequence‐Dependent DNA Damage Detection

Nair

Photochem & Photobiology

2013

Self Cite

The exposure of DNA to ultraviolet (UV) radiation causes sequence-dependent damage. Thus, there is a need for an analytical technique that can detect damage in large numbers of DNA sequences simultaneously. In this study, we have designed an assay for UVC-induced DNA damage in multiple oligonucleotides simultaneously by using a 96-well plate and a novel automated sample mover. The UVC-induced DNA damage is measured using smart probes, analogs of molecular beacons in which guanosine nucleotides act as the fluorescence quencher. Our results show that the oligonucleotide damage constants obtained with this method are reproducible and similar to those obtained in cuvettes. The calibration curve for poly-dT shows good linearity (R(2) = 0.96), with limits of detection (LOD) and quantification (LOQ) equal to 55 and 183 nm, respectively. The results show that the damage kinetics upon irradiation is sensitive to the different types of photoproducts formed in the different sequences used; i.e. poly-A oligonucleotides containing guanine are damaged at a faster rate than poly-A oligonucleotides containing either thymine or cytosine. Thus, detecting DNA damage in a 96-well plate and quantifying the damage with smart probes are a simple, fast and inexpensive mix-and-read technique for multiplexed, sequence-specific DNA damage detection.