Combined NMR and DFT Studies for the Absolute Configuration Elucidation of the Spore Photoproduct, a UV-Induced DNA Lesion

Abstract

By irradiation of bacterial spores under UV radiation, a photoproduct (SP) bearing a covalent methylene link between two adjacent thymines is formed in DNA. Because of the presence of an asymmetric carbon on the aglycone and of two possible orientations for the formation of the cross-link, four isomers could in principle be obtained. Currently, no conclusive structural information of this photoproduct is available. The structure of the isolated SPTpT dinucleotide was revisited in order to determine the type of cross-link and the absolute configuration of the C5a carbon. For this purpose, a study combining NMR spectroscopy and DFT calculations was pursued on the spore photoproduct of the dinucleoside TpT since its structure was previously shown to be identical to the one produced in DNA. A full characterization of SPTpT by NMR analyses was performed in D2O and DMSO. 2D NMR measurements (1H-13C, 1H-31P, COSY, NOESY, and ROESY) and DFT calculations (geometries optimization of R and S isomers and theoretical chemical shifts) lead us to conclude without ambiguity that the absolute configuration of the C5a carbon is R and that the methylene bridge of the photoproduct corresponds to the methyl group of the thymine located on the 3'-end of the dinucleoside monophosphate.

Photosensitised pyrimidine dimerisation in DNA

“…Interestingly, DNA double helix structure induces a highly stereospecific formation of SP photoproducts (Fig. 6); 87 their stucture has been recently assigned by 2D NMR studies combined with DFT calculations. Thus, the natural SP results from addition of the 55 thymine methyl group located on the 3´-end to the thymine C5 carbon located in the 5´-end, giving rise to a new chiral center with R absolute configuration.…”

“…Thus, the natural SP results from addition of the 55 thymine methyl group located on the 3´-end to the thymine C5 carbon located in the 5´-end, giving rise to a new chiral center with R absolute configuration. 87 Moreover, SP is only obtained as a Thy homodimer and has been detected both as intrastrand and interstrand lesion. 88, 89 60 Indeed, SP is a quite peculiar bipyrimidine photoproduct, whose formation has been related to three important factors: MePyPS, Fig.…”

Preparation and characterization of highly stable lipid nanoparticles with amorphous core of tuneable viscosity

“…An aliquot of each LNP aqueous dispersion is filled in an NMR tube and accurately weighted quantities of 0.1% w/w DSS in deuterated water (or 0.1% w/w TMS in chloroform) are added. The assignment of the 1 H resonances of PEG-40-stearate (Myrj s40™), lecithin and glycerides mixtures (soybean oil and Suppocire NC™) as pristine commercial ingredients is done by classical 1D and 2D methods such as 1 H-1 H homonuclear COSY and NOESY [24].…”

Crystal Structures and Repair Studies Reveal the Identity and the Base‐Pairing Properties of the UV‐Induced Spore Photoproduct DNA Lesion

“…[10] We report here the development of a synthesis of the 5S-and 5R-configured 5'!3' reaction products as phosphoramidite building blocks, their incorporation into oligonucleotides, and repair studies, now with full oligonucleotides. Our prepared lesions are again analogues that lack the central phosphodiester group to abbreviate the long and challenging synthesis of the natural spore lesion, as well as to ease the analysis of the repair reaction, which gives with our analogues an easy-to-detect strand break.…”