title: Electronic coupling between cytosine bases in DNA single strands  and i-motifs revealed from synchrotron radiation circular  dichroism experiments.
abstract: In this work we have recorded synchrotron radiation circular dichroism (SRCD) spectra from 180 nm to 360 nm of cytosine strands [(dC)(n), n = 1, 2, ..., 10] in aqueous solution at different pH values to reveal electronic coupling between bases in different ionisation states. The geometry of the strands is determined by the pH value and the strand length and the local organisation of the cytosines will determine the base-to-base interaction that impacts on the CD signal. At low pH where all bases are protonated, there is no signature of electronic coupling between the bases, and the SRCD spectrum is simply n times that of the n = 1 spectrum. At higher pH where all bases are neutral, the spectra for n > 1 differ from the monomer spectrum, which implies electronic coupling between bases. The correlation between the CD signal and n is linear, and the spatial extent of the excited state wavefunction is therefore over just two stacked bases both in the UV and VUV. At intermediate pH, the low-n spectra are different from the high-n spectra, and a transition is seen to occur at n = 6-8. We ascribe this behavior to the formation of i-motif structures between four (dC)(n) strands for high n.
authors.affiliation: Department of Physics, Stockholm University, AlbaNova University Center, S-10691 Stockholm, Sweden. aish@fysik.su.se
authors.forename: Anne I S
authors.initials: AI
authors.lastname: Holm
authors.forename: Lisbeth M
authors.initials: LM
authors.lastname: Nielsen
authors.forename: Bern
authors.initials: B
authors.lastname: Kohler
authors.forename: Søren Vrønning
authors.initials: SV
authors.lastname: Hoffmann
authors.forename: Steen
authors.initials: S
authors.lastname: Brøndsted Nielsen
mesh_terms: D002942:Circular Dichroism; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D017356:Synchrotrons
chemical_list: D003596:Cytosine; D004247:DNA