ArticleRNA (New York, N.Y.)2010
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- Tryptophan As a New Member of RNA-Induced Silencing Complexes Prevents Colon Cancer Liver Metastasis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- A crescendo of competent coding (c3) contains the Standard Genetic Code.RNA (New York, N.Y.) · 2022Article
- Big on Change, Small on Innovation: Evolutionary Consequences of RNA Sequence Duplication.Journal of molecular evolution · 2019Article
- The Genetic Code and RNA-Amino Acid Affinities.Life (Basel, Switzerland) · 2017Review
- Searching for a DNAzyme Version of the Leadzyme.Journal of molecular evolution · 2015Article
- A realistic model under which the genetic code is optimal.Journal of molecular evolution · 2013Article
- Selectionist and evolutionary approaches to brain function: a critical appraisal.Frontiers in computational neuroscience · 2012Article
- A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana.The Plant cell · 2011Article
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
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. Biochemical studies in several systems-including the hammerhead ribozyme and the purine riboswitch-find additional elements, such as loop-loop interactions, required for function yet not phylogenetically conserved. 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. Random insertion testing for site sufficiency seems likely to be broadly revealing.
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