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Statements

Subject Item
n2:RIV%2F61388963%3A_____%2F10%3A00353565%21RIV11-MSM-61388963
rdf:type
n13:Vysledek skos:Concept
dcterms: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.
dcterms: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
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
skos:notation
RIV/61388963:_____/10:00353565!RIV11-MSM-61388963
n3:aktivita
n7:P n7:Z
n3:aktivity
P(ME09019), Z(AV0Z40550506)
n3:cisloPeriodika
10
n3:dodaniDat
n11:2011
n3:domaciTvurceVysledku
n14:3237907
n3:druhVysledku
n18:J
n3:duvernostUdaju
n16:S
n3:entitaPredkladatele
n17:predkladatel
n3:idSjednocenehoVysledku
275569
n3:idVysledku
RIV/61388963:_____/10:00353565
n3:jazykVysledku
n10:eng
n3:klicovaSlova
SELEX; molecular modeling; aptamer; evolution; tryptophan
n3:klicoveSlovo
n6:molecular%20modeling n6:SELEX n6:aptamer n6:tryptophan n6:evolution
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[CB1BA2DF086A]
n3:nazevZdroje
R N A
n3:obor
n15:CC
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
10
n3:projekt
n8:ME09019
n3:rokUplatneniVysledku
n11:2010
n3:svazekPeriodika
16
n3:tvurceVysledku
Widmann, J. Chocholoušová, Jana Illangasekare, M. McDonald, D. Reeder, J. Knight, R. Iyer, M. Majerfeld, I. Malaiya, V. Yarus, M.
n3:wos
000281846500006
n3:zamer
n9:AV0Z40550506
s:issn
1355-8382
s:numberOfPages
10