Dye-induced aggregation of single stranded RNA: a mechanistic approach

Arch Biochem Biophys. 2006 Aug 15;452(2):93-101. doi: 10.1016/j.abb.2006.06.021. Epub 2006 Jul 12.

Abstract

The binding of proflavine (D) to single stranded poly(A) (P) was investigated at pH 7.0 and 25 degrees C using T-jump, stopped-flow and spectrophotometric methods. Equilibrium measurements show that an external complex PD(I) and an internal complex PD(II) form upon reaction between P and D and that their concentrations depend on the polymer/dye concentration ratio (C(P)/C(D)). For C(P)/C(D)<2.5, cooperative formation of stacks external to polymer strands prevails (PD(I)). Equilibria and T-jump experiments, performed at I=0.1M and analyzed according to the Schwarz theory for cooperative binding, provide the values of site size (g=1), equilibrium constant for the nucleation step (K( *)=(1.4+/-0.6)x10(3)M(-1)), equilibrium constant for the growth step (K=(1.2+/-0.6)x10(5)M(-1)), cooperativity parameter (q=85) and rate constants for the growth step (k(r)=1.2x10(7)M(-1)s(-1), k(d)=1.1 x 10(2)s(-1)). Stopped-flow experiments, performed at low ionic strength (I=0.01 M), indicate that aggregation of stacked poly(A) strands do occur provided that C(P)/C(D)<2.5.

MeSH terms

  • Binding Sites
  • Computer Simulation
  • Fluorescent Dyes
  • Kinetics
  • Macromolecular Substances / chemistry
  • Models, Chemical*
  • Models, Molecular*
  • Proflavine / analysis*
  • Proflavine / chemistry*
  • RNA, Messenger / analysis*
  • RNA, Messenger / chemistry*
  • Spectrometry, Fluorescence / methods*

Substances

  • Fluorescent Dyes
  • Macromolecular Substances
  • RNA, Messenger
  • Proflavine