title: Investigating local conformations of double-stranded DNA by low-energy circular dichroism of pyrrolo-cytosine.
abstract: Local base stacking and conformational mobility play a major role in the structure and function of nucleic acids. We have recently shown that the low-energy CD spectrum of 2-aminopurine (2-AP), i.e., the CD spectral region above 300 nm, can be used to monitor conformational changes in polynucleotides at or near mono- and dinucleotide 2-AP residues that replace adenine residues in DNA and RNA. Here, we extend this technique to pyrrolo-cytosine (PC), a fluorescent analogue of cytosine. The low-energy CD spectrum of a PC dinucleotide in dsDNA exhibits an exciton couplet with two bands of opposite sign centered at 350 nm. This signal is characteristic of base stacking between adjacent PC residues in a right helical conformation. Isolated PC nucleotide residues inserted into polynucleotide chains also display chirality that reflects the asymmetric environment of their sequence context. Thus, we show that the low-energy CD spectra of C(PC)A and A(PC)C sequences in dsDNA have opposite signs. It appears that the measurement of the low-energy CD spectra of PC residues will usefully complement 2-AP measurements by serving to characterize the local conformations and dynamics of nucleic acids near C residues and G-C base pairs.
authors.affiliation: Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, 205 route de Narbonne, 31077 Toulouse, France. neil@ipbs.fr
authors.forename: Neil P
authors.initials: NP
authors.lastname: Johnson
authors.forename: Walter A
authors.initials: WA
authors.lastname: Baase
authors.forename: Peter H
authors.initials: PH
authors.lastname: von Hippel
mesh_terms: D002942:Circular Dichroism / Q000379:methods*; D003596:Cytosine / Q000031:analogs & derivatives*; D004247:DNA / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D015341:Nucleic Acid Probes / Q000378:metabolism*; D009841:Oligonucleotides
chemical_list: D015341:Nucleic Acid Probes; D009841:Oligonucleotides; C486438:pyrrolo-deoxycytosine; D003596:Cytosine; D004247:DNA