Ethidium and proflavine binding to a 2',5'-linked RNA duplex.
Despite over 40 years of physical investigations, fundamental questions persist regarding the energetics of RNA and DNA intercalation. The dramatic unwinding of a nucleic acid duplex upon intercalation immediately suggests that the nucleic acid backbone should play a significant role in dictating the free energy of intercalation. However, the contribution of the backbone to intercalation free energy is difficult to appreciate given the intertwined energetics associated with intercalation (e.g., pi-pi stacking and solvent effects). Fluorescence titrations were used to determine the association constants of two known intercalators, proflavine and ethidium, for duplex 2',5'-linked RNA. Proflavine was found to bind 2',5' RNA with an association constant 25-fold greater than that measured for standard, 3',5'-linked RNA. In contrast, ethidium binds 2',5' RNA less favorably than standard RNA.
Horowitz
Eric D
ED
School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
Hud
Nicholas V
NV
D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D004996:Ethidium / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011370:Proflavine / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
D007364:Intercalating Agents; D012313:RNA; D004247:DNA; D011370:Proflavine; D004996:Ethidium