Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0angstroms resolution

Assignment of the hydrogen bonded proton resonances in (Escherichia coli) tRNAGlu by sequential melting

The 300 MHz nuclear magnetic resonance peaks from the hydrogen bonded protons in (Escherichia coli) tRNA(Glu) in Mg(++) solutions have been measured at temperatures between 25 degrees and 74 degrees . Between 25 degrees and 49 degrees four resonances broaden, three of which are assigned to the hU arm and one to a G.C pair of the tertiary structure. By 64 degrees these four resonances have disappeared and the nuclear magnetic resonance spectrum is fitted very well by a computer simulation based upon resonances from the acceptor, T-Psi-C, and anticodon arms. At 66 degrees the resonances from the T-Psi-C arm are lost and at 74 degrees only those from the anticodon are left. All 20 resonances expected from the cloverleaf model have been assigned by comparing the calculated positions of resonances in a particular arm with the stepwise loss of intensity with temperature. The root mean square error between calculated and observed positions is 0.17 ppm. Resonances at the end of helical regions which are sensitive to stacking beyond the helix allow us to conclude that the acceptor arm is stacked upon the T-Psi-C in a regular helix and that G [unk]73 is stacked upon base pair [unk]1-72 but the hU and anticodon arms are not stacked in a regular helix upon the intervening base A [unk]27.

Correlation between three-dimensional structure and chemical reactivity of transfer RNA

The bases of yeast tRNA(Phe) which react with carbodiimide and methoxyamine have been determined and this information has been combined with chemical modification studies of other workers to produce a composite picture of base accessibility in this tRNA. The results are compared with the three-dimensional structure which we have recently determined. The bases which react chemically lie in exposed positions in the three-dimensional model and those which do not are either in the double helical stem regions or else are involved in maintaining the tertiary structure through pairing or stacking interactions.

Studies of transfer RNA tertiary structure of singlet-singlet energy transfer

Five species of tRNAs bearing two different fluorescent groups were synthesized. These were suitable for intramolecular distance measurements by singlet-singlet energy transfer. The efficiency of energy transfer was determined from the sensitized emission of the energy acceptor. With the assumption that the relative orientation of donor and acceptor is random, the apparent distances between the 5'-end and the 3'-end, the 4-thiouridine and the 3'-end, the pseudouridine and 3'-end, the pseudouridine and the dihydrouridine in Escherichia coli formyl methionine tRNA, and between the 2-thiouridine (in the anticodon) and the 3'-end in E. coli glutamate tRNA were calculated to be 24 A, 38 A, 55 A, 36 A, and >65 A, respectively.

The molecular structure of yeast phenylalanine transfer RNA in monoclinic crystals

The molecular structure of monoclinic crystals of yeast phenylalanine tRNA is analyzed by comparing it to the orthorhombic crystals of the same material whose structure has been determined. Changing the packing of the molecule from the head-to-head, tail-to-tail arrangement in the orthorhombic lattice to a head-to-tail packing makes it possible to generate a proposed structure for the monoclinic unit cell. The structure factors for the proposed arrangement have been calculated and compared with those experimentally observed from monoclinic crystals. The residuals from this comparison are low enough to conclude that at 4-A resolution, the three-dimensional structure of the molecule in the monoclinic crystal is essentially the same as that in the orthorhombic crystal. In addition, a correlation coefficient calculated from intensities based on a skeletal model of the molecule also confirmed the structure in the monoclinic cell. Electron density difference maps, as well as the presence of close contacts in the anticodon loop region of the monoclinic crystal, suggest that the anticodon loop may have a slightly different conformation than that observed in the orthorhombic crystals.