title: Deoxycytidine methylation does not affect DNA.RNA hybrid formation or B-A transitions of (dG)n.(dC)n sequences.
abstract: Optical thermal denaturation and circular dichroism (CD) experiments were performed with the following non-selfcomplementary duplex DNA, RNA and DNA.RNA hybrids: (I) dGAG3C3G3CTC.dGAGC3G3C3TC, (II) dGAG3m5C3G3m5CTC.dGAGm5C3G3m5C3TC, (III) rGAG3C3G3CUC.rGAGC3G3C3UC, (IV) dGAG3C3G3CTC.rGAGC3G3C3UC, (V) rGAG3C3G3CUC.dGAGC3G3C3TC, (VI) dGAG3m5C3G3m5CTC.rGAGC3G3C3UC, (VII) rGAG3C3G3CUC.dGAGm5C3G3m5C3TC. Duplex stabilities (delta G degrees at 60 degrees C) increase in the order: I less than IV less than II = V = VI less than VII less than III. Large enthalpic stabilization is associated with intrastrand stacking of guanosine (rG) residues. CD spectroscopy indicates B-form conformations for the unmethylated and methylated DNA (I,II), A-form geometry for the RNA (III), and DNA.RNA hybrid (IV - VII) conformations resembling but not identical to A-RNA. C5-methyldeoxycytidine does not significantly influence DNA conformation, DNA.RNA hybrid formation, or the ability of DNA to adopt an A-type conformation in trifluoroethanol solutions.
authors: Department of Chemistry, University of California, Berkeley 94720.
authors: G T
authors: GT
authors: Walker
mesh_terms: D001482:Base Composition / Q000187:drug effects; D001483:Base Sequence; D002942:Circular Dichroism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D003841:Deoxycytidine / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009693:Nucleic Acid Hybridization / Q000187:drug effects; D013816:Thermodynamics; D014270:Trifluoroethanol / Q000494:pharmacology
chemical_list: D003841:Deoxycytidine; D014270:Trifluoroethanol; D004248:DNA (Cytosine-5-)-Methyltransferases