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dc.contributor.authorGevertz, Jana L.
dc.contributor.authorGan, Hin Hark
dc.contributor.authorSchlick, Tamar
dc.date.accessioned2015-06-25T14:09:44Z
dc.date.available2015-06-25T14:09:44Z
dc.date.issued2005
dc.identifier.citationGEVERTZ, JANA., GAN, HIN HARK & SCHLICK, TAMAR. (2005). In vitro RNA random pools are not structurally diverse: A computational analysis. RNA 2005 11: 853-863.en_US
dc.identifier.urihttp://dx.doi.org/10.1261/rna.7271405
dc.description.abstractIn vitro selection of functional RNAs from large random sequence pools has led to the identification of many ligand-binding and catalytic RNAs. However, the structural diversity in random pools is not well understood. Such an understanding is a prerequisite for designing sequence pools to increase the probability of finding complex functional RNA by in vitro selection techniques. Toward this goal, we have generated by computer five random pools of RNA sequences of length up to 100 nt to mimic experiments and characterized the distribution of associated secondary structural motifs using sets of possible RNA tree structures derived from graph theory techniques. Our results show that such random pools heavily favor simple topological structures: For example, linear stem–loop and low-branching motifs are favored rather than complex structures with high-order junctions, as confirmed by known aptamers. Moreover, we quantify the rise of structural complexity with sequence length and report the dominant class of tree motifs (characterized by vertex number) for each pool. These analyses show not only that random pools do not lead to a uniform distribution of possible RNA secondary topologies; they point to avenues for designing pools with specific simple and complex structures in equal abundance in the goal of broadening the range of functional RNAs discovered by in vitro selection. Specifically, the optimal RNA sequence pool length to identify a structure with x stems is 20x.en_US
dc.language.isoenen_US
dc.publisherRNA Societyen_US
dc.subjectIn vitro selectionen_US
dc.subjectRandom poolen_US
dc.subjectRNA secondary structureen_US
dc.subjectRNA topologyen_US
dc.subjectGraph theoryen_US
dc.subjectRNA pool designen_US
dc.titleIn vitro RNA random pools are not structurally diverse: A computational analysisen_US
dc.typeArticleen_US
dc.typeTexten_US
prism.publicationNameRNAen_US
prism.volume11
prism.startingPage853
prism.endingPage863
dc.identifier.handlehttps://dr.tcnj.edu/handle/2900/148


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