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From sequence to structure and function of non-coding RNA

According to the central dogma of molecular biology, RNA acts only as messenger RNA (mRNA) between the genomic DNA and protein biosynthesis ("DNA makes RNA makes protein"). Since several years, however, it is obvious that RNA can fulfill a variety of further biological functions during replication, transcription, localization, and degradation of biological macromolecules:

  • RNA can act as an enzyme.
  • Peptide bond formation in ribosomes is catalyzed by ribosomal RNA.
  • Cleavage and ligation of RNA can be catalyzed by RNA.
  • RNA may have a structural role.
  • The 7SL RNA forms together with several proteins the signal recognition particle, which influences the intracellular site of protein biosynthesis.
  • RNA may influence gene regulation.
  • Micro RNA (miRNA) is encoded genomically in many organisms and controls translation of mRNA.
  • Silencing RNA (siRNA) may initialize degradation of foreign RNA.
  • A riboswitch as element of a mRNA may regulate synthesis and function of an mRNA for example in dependence upon temperature or presence of small molecules.

This class of RNAs is termed non-coding RNA (ncRNA).

For the biological function of ncRNA not only their sequences but also their three-dimensional structure and their structural dynamics are critical. In the team we develop and test bioinformatic tools that are used for the search of ncRNAs in genomes and for prediction of structure, structural dynamics and function of ncRNAs. Examples are:

undefinedStrAl
a program for multiple alignment of RNA sequences taking into account their base-pairing probabilities.
undefinedDeniz, D., Wilm, A., Mainz, I. & Steger, G. (2006)
STRAL: Progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time.
Bioinformatics 22, 1593-1599.

undefinednovoMIR

is a program for the de novo prediction of pre-miRNA and miRNA/miRNA* regions in genomic plant DNA.

undefinedTeune, J.-H. & Steger, G. (2010)
novoMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome.
J. Nucleic Acids 2010.

undefinedConStruct
a tool for interactive alignment and consensus structure prediction of RNA.
undefinedLück, R., Gräf, S. & Steger, G. (1999)
ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure.
Nucleic Acids Research 27, 4208-4217.
undefinedWilm, A., Linnenbrink, K. & Steger, G. (2008)
ConStruct: improved construction of RNA consensus structures.
BMC Bioinformatics 9, 219.

undefinedBRAliBase
a "Benchchmark RNA Alignment database".
undefinedWilm, A., Mainz, I. & Steger, G. (2006)
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms for Molecular Biology 1, 19.

undefinedpoland
a web service for calculation of the thermal stability of double-stranded nucleic acids (DNA, dsRNA, RNA/DNA hybrids)
undefinedSteger, G. (1994)
Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction.
Nucleic Acids Research 22, 2760-2768.

Publications

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