Intensity fluctuation spectroscopy and transfer RNA conformation. III. Influence of NaCl concentration on the size and shape of the initially salt‐free tRNA in solution

Abstract

SynopsisThe influence of sodium ion concentration in solution on the initially salt-free conformation of bulk tRNA from baker's yeast has been investigated by means of photon correlation spectroscopy. From the measured values of translational (DT) and rotational (DR) diffusion coefficients, the semiaxes of an ellipsoid of revolution, which are hydrodynamically equivalent to the tRNA molecule, were calculated for tRNA solutions in pure HzO as well as in 0.005, 0.1, 0.5M NaCl and 0.01M MgClz solutions a t pH 4.2 and 7.5. These data, combined with our previous studies, suggested a model which describes the formation of an ordered tRNA structure due to increasing NaCl concentrations. Furthermore, we have obtained information concerning intermolecular interactions between tRNA molecules in solution. In low-salt or salt-free tRNA solutions, we detected in the linewidth distribution function an extra-fast component which can be attributed as possibly due to charge fluctuations related to the reaction of ionization of organic bases. In our light-scattering linewidth measurements, we do not see fluctuations of charged and uncharged states directly as concentration fluctuations. Rather, we postulate a modulation of long-range intermolecular electrostatic interactions between the tRNA molecules due to such charge fluctuations. It is this modulation which is related to the fast component of the time correlation function a t finite concentrations. A quantitative theory is needed to provide a more definitive explanation of the dynamical behavior of tRNA in salt-free or low-salt solutions.

Studies of protein–nucleic acid interactions by photon correlation spectroscopy. I. tRNA–BSA interactions at low ionic strength

“…3. The observed increase of the D2 value with increasing scattering angles is similar to the dependence observed in the case of low-salt tRNA solutions 15 and can be attributed to electrostatic intermolecular interactions. There are two kinds of aggregates formed in tRNA-BSA solutions.…”

“…15,17 For each of the BSA solutions the correlation function of scattered light was measured at the scattering angle 8 =91.13 0 . The net experimental function after base line subtraction was then fitted using a single exponential function g<tl (7) = exp( -r s7) (8) and the method of cumulants 18…”

“…15 BSA fraction V t6 (Sigma Chemical Company, Product No. A4503) was purified by gel filtration through a Sephadex G-I00 column in ImM sodium cacodylate buffer at pH 6.0 adjusted with CHsCOOH.…”

Complete nuclear magnetic resonance signal assignments and initial structural studies of [13C]methyl-enriched yeast transfer ribonucleic acid

“…Not surprisingly, given the simplistic nature of the model, tr values are not the same for all methyl groups. They range from 10 to 20 ns, the latter being fairly close to other values for tRNA under similar conditions (20-30 ns) (Schmidt & Edelheit, 1981; Patkowski & Chu, 1979;Schmidt et al, 1983;Hamill et al, 1980). Presumably, low values of rR reflect some independent motion of bases or sections of the macromolecule.…”

Photon correlation spectroscopy and light scattering of eye lens proteins at high concentrations

“…These results were criticized by Ackerson (Ackerson, 1978). At the same time, the interpretation of light-scattering results is complicated for many systems due to the fact that clusters are formed at higher concentrations (Bauter, 1980;Giordano et al, 198 la, b;Patkowski et al, 1979Patkowski et al, , 1980van Helden and Vrij, 1980).…”