Binding of spermidine to transfer ribonucleic acid

Abstract

The binding of spermidine to yeast tRNAPhe and Escherichia coli tRNAGlu2 at low and high ionic strength was studied by equilibrium dialysis. Once corrected for the expected Donnan effect, the binding at low ionic strength obeys the simple relationship of equivalent binding sites, and cooperative binding of spermidine to tRNA could not be detected. At low ionic strength (0.013 M Na+ ion), tRNAPhe (yeast) has 13.9 +/- 2.3 strong spermidine binding sites per molecule with Kd = 1.39 X 10(-6) M and a few weak spermidine binding sites which were inaccessible to experimentation; tRNAGlu2 (E. coli) has 14.8 +/- 1.6 strong spermidine binding sites and 4.0 +/- 0.1 weak spermidine binding sites with Kd = 1.4 X 10(-6) M and Kd = 1.23 X 10(-4) M, respectively. At high ionic strength (0.12 M monovalent cation) and 0.01 M Mg2+, tRNAPhe (yeast) has approximately 13 strong spermidine binding sites with an apparent Kd = 3.4 X 10(-3) M while the dimeric complex tRNAPhe X tRNAGlu2 has 10.4 +/- 1.2 strong spermidine binding sites per monomer with an apparent Kd = 2.0 X 10(-3) M. In the presence of increasing Na+ ion or K+ ion concentration, spermidine binding data do not fit a model for competitive binding to tRNA by monovalent cations. Rather, analysis of binding data by the Debye-Hückel approximation results in a good fit of experimental data, indicating that monovalent cations form a counterion atmosphere about tRNA, thus decreasing electrostatic interactions. On the basis of equilibrium binding analyses, it is proposed that the binding of spermidine to tRNA occurs predominantly by electrostatic forces.

Endogenous polyamine function—the RNA perspective

“…Using capillary electrophoresis the affinities of polyamines for tRNA were calculated to be 8.7 × 10 −5 M, 6.1 × 10 −5 M and 1.0 × 10 −5 M for spermine, spermidine and putrescine, respectively ( 129 ). These affinities are in the range of the equilibrium dissociation constants calculated for polyamine binding to tRNA Phe and tRNA Glu based on equilibrium dialysis binding data gathered under low ionic strength conditions ( 130 ). Furthermore, positive cooperativities of binding were detected (Hill coefficients: 1.42, 1.14, 1.12, respectively).…”

Thermodynamics of the DNA binding of biogenic polyamines: Calorimetric and spectroscopic investigations

“…Structurally, polyamines have cationic groups (figure 1) with multiple positive charges (four for spermine, three for spermidine, two each for putrescine and cadaverine) that enable them to interact with anionic nucleic acids protecting the latter from damaging agents [23][24][25][26]. A number of studies have been performed to understand the in vitro interaction of polyamines and their derivatives with DNA and RNA by a variety of techniques, such as equilibrium dialysis, NMR imaging, circular dichroism, Raman spectroscopy, FT IR spectroscopy, X-ray crystallography and differential scanning calorimetry [27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42]. These studies have advanced that electrostatic binding to be the leading mode of interaction among the various binding forces involved.…”

Influence of the polyamines spermine and spermidine on yeast tRNAphe as revealed from its imino proton NMR spectrum

“…These findings have raised some interest in the binding properties of pol-Nucleic Acids Research yamines to tRNA and as a result a number of studies on the interaction of polyamines with tRNA have been published [7][8][9][10][11][12][13][14][15][16][17]. Equilibrium binding studies have been performed to establish the nature and strength of polyamine binding [7][8][9] but the data were evaluated without taking electrostatic contributions into account.…”

“…Equilibrium binding studies have been performed to establish the nature and strength of polyamine binding [7][8][9] but the data were evaluated without taking electrostatic contributions into account. Indeed, a recent study has indicated that electrostatic contributions to the binding cannot be neglected [10]. Structural information on polyamine binding is available from X-ray studies by which the location of two spermine molecules in crystals of tRNAPhe from yeast could be determined [11].…”