Osmolytes and macromolecular crowders have the potential to influence the stability of secondary structure motifs and alter preferences for conserved nucleic acid sequences in vivo. To further understand the cellular function of RNA we observed the effects of a model osmolyte, polyethylene glycol (PEG) 200, and a model macromolecular crowding agent, PEG 8000, on the GAAA tetraloop motif. GAAA t...

The major determinant for the identity of alanine tRNAs is a single base pair in the acceptor helix that is proximal to the site of amino acid attachment. A 7-base-pair microhelix that recreates the acceptor helix can be charged with alanine. No other examples of charging of small helices with specific amino acids have been reported, to our knowledge. We show here that a 13-base-pair and an 8-b...

Leucyl-tRNA synthetase (LeuRS), one of the class Ia aminoacyl-tRNA synthetases, joins Leu to tRNA(Leu) and excludes noncognate amino acids in protein synthesis. In this study, Escherichia coli LeuRS mutants at amino acid E292, which was located in the connective polypeptide 1 insertion region, were synthesized. Although mutated LeuRS showed little change in structure compared with wild-type Leu...

Identity elements of tRNA(Thr) towards Saccharomyces cerevisiae threonyl-tRNA synthetase were examined using in vitro transcripts. By mutation studies, a marked decrease in aminoacylation with threonine showed that the first base pair in the acceptor stem and the second and third positions of the anticodon are major identity elements of tRNA(Thr), which are essentially the same as those of Esch...

By a lattice we shall always mean a distributive lattice which is bounded, i.e. has both a bottom element 0 and a top element 1. Lattice homomorphisms will always be assumed to preserve 0 and 1. By a modality on a (distributive) lattice L = (L, ∧, ∨, ≤, 0, 1) is meant a map : L → L satisfying (1) 1 = 1, (2) (x ∧ y) = x ∧ y for x, y ∈ L. The pair (L, ) will be called a modalized (distributive) l...

Mutations induced by one of the typical dietary mutagens/carcinogens, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), were characterized using gpt delta transgenic mice. This transgenic mouse model has two selection methods to efficiently detect different types of mutations, i.e. 6-thioguanine selection for point mutations and Spi(-) selection for deletions. The mice were fed with a die...

Uracil (U) can be found in DNA as a mismatch paired either to adenine (A) or to guanine (G). Removal of U from DNA is performed by a class of enzymes known as uracil-DNA-glycosylases (UDG). Recent studies suggest that recognition of U-A and U-G mismatches by UDG takes place via an extra-helical mechanism. In this work, we use molecular dynamics simulations to analyze the structure, dynamics and...