title: Stacking interactions of ApA analogues with modified backbones.
abstract: CD spectra have been measured as a function of temperature for a number of ApA analogues with modified backbones. Oligonucleotides with these modified backbones are being used as antisense agents having potential as viral therapeutics. Results of these studies show that when a carbonyl is substituted for the phosphate to produce an uncharged backbone, the analogues that have either sugar or morpholino substitution do not stack. In contrast, when a morpholino group is substituted for the sugar and the phosphate is modified so as to be uncharged, there is strong base stacking. Stacking interactions in the phosphorus-linked morpholino analogues are at least as strong as those found in d(ApA). The stacking interactions in ApA are weak by comparison. Singular value decomposition demonstrates that the stacking is two state, and Taylor series decomposition yields a coefficient that measures base stacking interactions. The van't Hoff equation is applied to the base stacking coefficient from the Taylor series fitting to give thermodynamic parameters.
authors.affiliation: Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331.
authors.forename: H
authors.initials: H
authors.lastname: Kang
authors.forename: P J
authors.initials: PJ
authors.lastname: Chou
authors.forename: W C
authors.initials: WC
authors.lastname: Johnson
authors.forename: D
authors.initials: D
authors.lastname: Weller
authors.forename: S B
authors.initials: SB
authors.lastname: Huang
authors.forename: J E
authors.initials: JE
authors.lastname: Summerton
mesh_terms: D002942:Circular Dichroism; D015226:Dinucleoside Phosphates / Q000737:chemistry*; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D015226:Dinucleoside Phosphates; C020269:2'-deoxyadenylyl-(3'-5')-2'-deoxyadenosine; C026520:adenosine monophosphate-adenosine