Stable tRNA-based phylogenies using only 76 nucleotides

initiator tRNA analogs with different nucleotides in the

The ef fec t of base changes a t the fourth pos i t ion from the 3 ' terminus of Esoheriohia c o l i i n i t i a t o r tRNA has been s tudied to t e s t the ' d i s criminator hypothesis ' which proposed tha t the nucleot ide in t h i s pos i t ion might have a r o l e i n the s p e c i f i c i t y of the aminoacylation r eac t ion . £ . ool i i n i t i a t o r tRNA lacking the 3 ' t e rmina l ...

Rapid determination of nucleotides that define tRNA(Gly) acceptor identity.

Expression of the genetic code depends on the recognition of specific tRNAs by the enzymes that aminoacylate them. A computer comparison of tRNA sequences coupled with analysis of mutant nonsense-suppressor tRNAs has revealed the structural features that distinguish the acceptor identity of Escherichia coli tRNA(Gly) from tRNAs that accept phenylalanine, arginine, lysine, and glutamine. On repl...

Reconstructing and Using Phylogenies

DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides

Single-stranded DNA molecules have the capacity to adopt catalytically active structures known as DNAzymes, although the fundamental limits of this ability have not been determined. Starting with a parent DNAzyme composed of all four types of standard nucleotides, we conducted a search of the surrounding sequence space to identify functional derivatives with catalytic cores composed of only thr...

Finding Cognate Groups Using Phylogenies

A central problem in historical linguistics is the identification of historically related cognate words. We present a generative phylogenetic model for automatically inducing cognate group structure from unaligned word lists. Our model represents the process of transformation and transmission from ancestor word to daughter word, as well as the alignment between the words lists of the observed l...