Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic study.
Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches is monitored using temperature-dependent optical absorption spectroscopy. A sequential three-state equilibrium model is used to analyze the measured melting profiles and evaluate thermodynamic parameters associated with dissociation of the complexes. The free-energy of stabilization of a nick complex compared to a gap complex due to base stacking is determined to be -1.9 kcal/mol. The influence of a mispaired base in these systems is shown to destabilize a nick complex by 3.1 kcal/mol and a gap complex by 2.8 kcal/mol, respectively.
Murphy
Dierdre
D
Nanotechnology Group, NMRC, Lee Maltings, Prospect Row, Cork, Ireland.
Doyle
Hugh
H
Eritja
Ramon
R
Redmond
Gareth
G
D020137:Base Pair Mismatch; D020029:Base Pairing; D001483:Base Sequence; D004355:Drug Stability; D066298:In Vitro Techniques; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000235:genetics; D013053:Spectrophotometry; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides