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One and two dimensional NMR techniques have been used together with molecular modelling to obtain the solution structure for the photoproduct d(TpA)*. The NMR data confirm that the cyclobutane linkage is formed between the bonds thymine C6-C5 and adenine C5-C6. The 2D NOE data are used as constraints in a distance geometry calculation. The structures obtained show a trans-syn cyclobutane linkage and the glycosidic angles are SYN and ANTI for thymidine and deoxyadenosine, respectively. The coupling constant data are used to check the backbone torsion angles of the obtained structures. Typical torsion angles are a gamma+ and beta t for the deoxyadenosine residue. A free molecular dynamics simulation of a trans-syn d(TpA) photoproduct confirmed all these structural characteristics.

nucleic acids research

The solution structure of the intramolecular photoproduct of d(TpA) derived with the use of NMR and a combination of distance geometry and molecular dynamics