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Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA
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SYSNO ASEP 0353565 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA Author(s) Majerfeld, I. (US)
Chocholoušová, Jana (UOCHB-X) RID, ORCID
Malaiya, V. (US)
Widmann, J. (US)
McDonald, D. (US)
Reeder, J. (US)
Iyer, M. (US)
Illangasekare, M. (US)
Yarus, M. (US)
Knight, R. (US)Number of authors 10 Source Title RNA. - : Cold Spring Harbor Laboratory Press - ISSN 1355-8382
Roč. 16, č. 10 (2010), s. 1915-1924Number of pages 10 s. Language eng - English Country US - United States Keywords SELEX ; molecular modeling ; aptamer ; evolution ; tryptophan Subject RIV CC - Organic Chemistry R&D Projects ME09019 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) CEZ AV0Z40550506 - UOCHB-X (2005-2011) UT WOS 000281846500006 DOI 10.1261/rna.2220210 Annotation 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Year of Publishing 2011
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