Permanent dipole moment of tRNA's and variation of their structure in solution

Abstract

The structure of six different tRNA molecules has been analyzed in solution by electrooptical measurements and by bead model simulations. The electric dichroism measured as a function of the field strength shows that tRNA's are associated with substantial permanent dipole moments, which are in the range of 1 x 10(-27) cm(identical to 300 D; before correction for the internal directing field). Rotational diffusion time constants of tRNA molecules in their native state at 2 degrees C show a considerable variation. A particularly large value found for tRNA(Tyr) (50 ns) can be explained by its nine additional nucleotide residues. However, remarkable variations remain for tRNA molecules with the standard number of 76 nucleotide residues (tRNA(Phe) [yeast] 41.6 ns, tRNA(Val) [Escherichia coli] 44.9 ns, tRNA(Glu) [E. coli] 46.8 ns; tRNA(Phe) [E. coli] 48.3 ns). These variations indicate modulations of the tertiary structure, which may be due to a change of the L-hinge angle. Bead models are used to simulate both electric and hydrodynamic parameters of tRNA molecules according to the crystal structure of tRNA(Phe) (yeast). The asymmetric distribution of phosphate charges with respect to the center of diffusion leads, under the assumption of a constant charge reduction to 15% by ion condensation, to a theoretical dipole moment of 7.2 x 10(-28) cm, which is in reasonable agreement with the measurements. The dichroism decay curve calculated for tRNA(Phe) (yeast) is also consistent with the measurements and thus the structure in solution and in the crystal must be very similar in this case. However, our measurements also indicate that the structure of some other tRNA's in solution is different, even in cases with the same number of nucleotide residues.

Global Structure and Flexibility of Hairpin Ribozymes with Extended Terminal Helices

“…Here, we were interested in directly acquiring information on this angle using transient electric dichroism (TED). TED in its quantitative form has been used previously for the analysis of tRNAs (Porschke & Antosiewicz, 1990) and for studies of DNA (Porschke, 1991) and DNA-protein complexes Meyer-Almes et al, 1994). Its sensitivity and quanti®ability should make TED a well suited tool for studying hairpin ribozyme structure.…”

Computation of the dipole moments of proteins

“…Comparison of dipole moments calculated on the basis of assumed models of proteins with experimental results provides a good test of theoretical approaches and consequently has a significant influence on many areas of molecular biology. Dipole moments are also important for proper interpretation of the results of electrooptical relaxation experiments in terms of macromolecular structures (O'Konsky et al, 1959;Porschke, 1987; Antosiewicz, 1990).…”

Hydrodynamic properties of a double-helical model for DNA

“…In the early years of bead-model theory (Bloomfield et al, 1967;Garcia de la Torre and Bloomfield, 1977), it was thought that the beads in the model should be of macromolecular size (i.e., various orders of magnitude larger than the solvent molecules) to guarantee the validity of the continuum hydrodynamics in which the theory is based. However, bead models at a molecular scale, even with atomic resolution, were later used successfully for various biopolymers (Venable and Pastor, 1988;Porschke and Antosiewicz, 1990;Tirado et al, 1990). Indeed, the possibility of a bead model with high resolution for DNA, that would take into account the double-helical structure, was presented years ago (Garcia de la Horta, 1976, 1977), but unfortunately, experimental data on short DNA oligomers were not available by that time, and the theory was in its earliest stages.…”