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The biological role of RNA is delimited by its possible reactions, which can be explored by selection. A comparison of selected RNAs that bind one ligand with those that bind two related ligands suggests that a single nucleotide substitution can expand binding specificity. An RNA site with dual (joint) specificity has adenine and cytosine bases whose pKa's(More)
The canonical genetic code has been reported both to be error minimizing and to show stereochemical associations between coding triplets and binding sites. In order to test whether these two properties are unexpectedly overlapping, we generated 200,000 randomized genetic codes using each of five randomization schemes, with and without randomization of stop(More)
Messenger RNA's are translated in successive three-nucleotide steps (a reading frame), therefore decoding must proceed in only one of three possible frames. A molecular model for correct propagation of the frame is presented based on (i) the measured translational properties of transfer RNA's (tRNA's) that contain an extra nucleotide in the anticodon loop(More)
An RNA has been selected that rapidly aminoacylates its 2'(3') terminus when provided with phenylalanyl-adenosine monophosphate. That is, the RNA accelerates the same aminoacyl group transfer catalyzed by protein aminoacyl-transfer RNA synthetases. The best characterized RNA reaction requires both Mg2+ and Ca2+. These results confirm a necessary prediction(More)
We introduce three new computer programs and associated tools of the Delila nucleic-acid sequence analysis system. The first program, Module, allows rapid transportation of new sequence analysis tools between scientists using different computers. The second program, DBpull, allows efficient access to the large nucleic-acid sequence databases being collected(More)
Selection for amino acid affinity by elution of RNAs from tryptophan-Sepharose using free L-tryptophan evokes one sequence predominantly (K(D) = 12 microM), a symmetrical internal loop of 3 nt per side. Though we have also isolated larger sequences with affinity for tryptophan, successively squeezed selection in randomized tracts of 70, 60, 40, 20 and 17 nt(More)
Although functional RNA molecules are known to be biased in overall composition, the effects of background composition on the probability of finding a particular active site by chance has received little attention. The probability of finding a particular motif has important implications both for understanding the distribution of functional RNAs in ancient(More)
We have studied RNA binding to vesicles bounded by ordered and disordered phospholipid membranes. A positive correlation exists between bilayer order and RNA affinity. In particular, structure-dependent RNA binding appears for rafted (liquid-ordered) domains in sphingomyelin-cholesterol-1,2-dioleoyl-sn-glycero-3-phosphocholine vesicles. Binding to more(More)