title: Sequence-dependent emission from stacked forms of ApC and CpA. Evidence for stacked base ('dimer') absorption and left-handed stacked conformation.
abstract: The corrected and normalised emission spectrum, quantum yield and emission anisotropy are reported for partially stacked adenylyl-3',5'-cytidine (ApC) excited at 266 nm and are compared with cytidylyl-3',5'-adenosine (CpA). Utilizing characteristics determined independently for adenosine and cytidine-5'-monophosphate (CMP), the concurrent self-consistent resolution of emission spectrum and emission anisotropy has been carried out in two ways; first completely empirically as for CpA and second on the basis of a simple stacking model, with concordant results. The total emission spectrum of ApC is resolved into (i) components characteristic of the two monomers and (ii) a red-shifted complex emission. The complex emission spectrum, which is much stronger than from CpA and is complementary to it in bandshape, can also be satisfactorily described by the same components. The dimeric (A, C) system can exist in at least two luminescent stacked forms, proportions of which are determined by the overall stacked fraction and the population within this fraction of the various stacked conformers. The relation between the ratios of the components and the fractional absorption of the stacked forms indicates that the low-energy component is a (hetero-) dimer emission while the high energy component appears to be a true exciplex (hetero-excimer). Comparison with the circular dichroism and NMR literature shows a satisfactory semi-quantitative correlation with the hypothesis that the low energy (hetero-) dimer emission originates from a left-handed stacked conformation Mbb, while the higher energy hetero-excimer originates from the predominant right-handed stacked conformation Pba.
authors.affiliation: Department of Chemistry, Oregon State University, Corvallis 97331.
authors.forename: M
authors.initials: M
authors.lastname: Daniels
authors.forename: C S
authors.initials: CS
authors.lastname: Shaar
authors.forename: J P
authors.initials: JP
authors.lastname: Morgan
mesh_terms: D003568:Cytidine Monophosphate; D015226:Dinucleoside Phosphates; D009690:Nucleic Acid Conformation; D013050:Spectrometry, Fluorescence / Q000379:methods; D013053:Spectrophotometry / Q000379:methods
chemical_list: D015226:Dinucleoside Phosphates; C013907:cytidylyl adenosine; C013797:adenylyl cytidine; D003568:Cytidine Monophosphate