Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 - 4) vs. (2 + 2) adducts

Mahesh Hariharan, Karsten Siegmund, Clifton Saurel, Martin McCullagh, George C Schatz, Frederick D. Lewis

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The photochemical reactions of eleven synthetic DNA hairpins possessing a single TT step either in a base-paired stem or in a hexanucleotide linker have been investigated. The major reaction products have been identified as the cis-syn (2 + 2) adduct and the (6 - 4) adduct on the basis of their spectroscopic properties including 1D and 2D NMR spectra, UV spectra and stability or instability to photochemical cleavage. Product quantum yields and ratios determined by HPLC analysis allow the behaviour of the eleven hairpins to be placed into three groups: Group I in which the (2 + 2) adduct is the major product, as is usually the case for DNA, Group II in which comparable amounts of (2 + 2) and (6 - 4) adducts are formed, and Group III in which the major product is the (6 - 4) adduct. The latter behaviour is without precedent in natural or synthetic DNA and appears to be related to the highly fluxional structures of the hairpin reactants. Molecular dynamics simulation of ground state conformations provides quantum yields and product ratios calculated using a single parameter model that are in reasonable agreement with most of the experimental results. Factors which may influence the observed product ratios are discussed.

Original languageEnglish
Pages (from-to)266-271
Number of pages6
JournalPhotochemical and Photobiological Sciences
Volume13
Issue number2
DOIs
Publication statusPublished - 2014

Fingerprint

Thymine
thymine
adducts
Conformations
deoxyribonucleic acid
Quantum yield
DNA
products
Photochemical reactions
Molecular Dynamics Simulation
Reaction products
Ground state
Molecular dynamics
High Pressure Liquid Chromatography
Nuclear magnetic resonance
stems
reaction products
photochemical reactions
Computer simulation
cleavage

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Medicine(all)

Cite this

Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 - 4) vs. (2 + 2) adducts. / Hariharan, Mahesh; Siegmund, Karsten; Saurel, Clifton; McCullagh, Martin; Schatz, George C; Lewis, Frederick D.

In: Photochemical and Photobiological Sciences, Vol. 13, No. 2, 2014, p. 266-271.

Research output: Contribution to journalArticle

Hariharan, Mahesh ; Siegmund, Karsten ; Saurel, Clifton ; McCullagh, Martin ; Schatz, George C ; Lewis, Frederick D. / Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 - 4) vs. (2 + 2) adducts. In: Photochemical and Photobiological Sciences. 2014 ; Vol. 13, No. 2. pp. 266-271.
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