Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA

0353565 - ÚOCHB 2011 RIV US eng J - Journal Article
Majerfeld, I. - Chocholoušová, Jana - Malaiya, V. - Widmann, J. - McDonald, D. - Reeder, J. - Iyer, M. - Illangasekare, M. - Yarus, M. - Knight, R.
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.
RNA. Roč. 16, č. 10 (2010), s. 1915-1924. ISSN 1355-8382. E-ISSN 1469-9001
R&D Projects: GA MŠMT ME09019
Institutional research plan: CEZ:AV0Z40550506
Keywords : SELEX * molecular modeling * aptamer * evolution * tryptophan
Subject RIV: CC - Organic Chemistry
Impact factor: 6.051, year: 2010

Conservation is often used to define essential sequences within RNA sites. However, conservation finds only invariant sequence elements that are necessary for function, rather than finding a set of sequence elements sufficient for function. Here we define a critical test of sufficiency: We embed a minimal, apparently sufficient motif for binding the amino acid tryptophan in a random-sequence background and ask whether we obtain functional molecules. After a negative result, we use a combination of three-dimensional structural modeling, selection, designed mutations, high-throughput sequencing, and bioinformatics to explore functional insufficiency. This reveals an essential unpaired G in a diverse structural context, varied sequence, and flexible distance from the invariant internal loop binding site identified previously. Addition of the new element yields a sufficient binding site by the insertion criterion, binding tryptophan in 22 out of 23 tries.
Permanent Link: http://hdl.handle.net/11104/0192791