Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach

  • Uri Laserson
  • Hin Hark Gan
  • Tamar Schlick
Part of the Lecture Notes in Computational Science and Engineering book series (LNCSE, volume 49)


The central dogma of biology—that DNA makes RNA makes protein—was recently expanded yet again with the discovery of RNAs that carry important regulatory functions (e.g., metabolite-binding RNAs, transcription regulation, chromosome replication). Thus, rather than only serving as mediators between the hereditary material and the cell’s workhorses (proteins), RNAs have essential regulatory roles. This finding has stimulated a search for small functional RNA motifs, either embedded in mRNA molecules or as separate molecules in the cell. The existence of such simple RNA motifs in Nature suggests that the results from experimental in vitro selection of functional RNA molecules may shed light on the scope and functional diversity of these simple RNA structural motifs in vivo. Here we develop a computational method for extracting structural information from laboratory selection experiments and searching the genomes of various organisms for sequences that may fold into similar structures (if transcribed), as well as techniques for evaluating the structural stability of such potential candidate sequences. Applications of our algorithm to several aptamer motifs (that bind either antibiotics or ATP) produce a number of promising candidates in the genomes of selected bacterial and archaeal species. More generally, our approach offers a promising avenue for enhancing current knowledge of RNA’s structural repertoire in the cell.


Candidate Sequence Archaeal Genome Minimum Energy Structure Natural RNAs Suboptimal Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Uri Laserson
    • 1
    • 2
  • Hin Hark Gan
    • 1
  • Tamar Schlick
    • 1
    • 2
  1. 1.Department of ChemistryNew York UniversityNew YorkUSA
  2. 2.Courant Institute of Mathematical SciencesNew York UniversityNew YorkUSA

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