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

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	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. 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. (en)
Title	Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA (en)
skos:prefLabel	Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA (en)
skos:notation	RIV/61388963:_____/10:00353565!RIV11-MSM-61388963
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(ME09019), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	10
http://linked.open...vai/riv/dodaniDat	2011
http://linked.open...aciTvurceVysledku	Chocholoušová, Jana
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	275569
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/10:00353565
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	SELEX; molecular modeling; aptamer; evolution; tryptophan (en)
http://linked.open.../riv/klicoveSlovo	aptamer evolution molecular modeling tryptophan SELEX
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[CB1BA2DF086A]
http://linked.open...i/riv/nazevZdroje	R N A
http://linked.open...in/vavai/riv/obor	CC
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	10 (xsd:int)
http://linked.open...vavai/riv/projekt	Theoretical investigation of RNA structure, dynamics and function and their relationship.
http://linked.open...UplatneniVysledku	2010
http://linked.open...v/svazekPeriodika	16
http://linked.open...iv/tvurceVysledku	Chocholoušová, Jana Iyer, M. Knight, R. McDonald, D. Widmann, J. Illangasekare, M. Majerfeld, I. Malaiya, V. Reeder, J. Yarus, M.
http://linked.open...ain/vavai/riv/wos	000281846500006
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	1355-8382
number of pages	10 (xsd:int)
is http://linked.open...avai/riv/vysledek of	Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA

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