Spectral Graph Partitioning Analysis of In Vitro Synthesized RNA Structural Folding

  • Stanley NG Kwang Loong
  • Santosh K. Mishra
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4146)


In this paper, we investigate the topological properties of synthetic RNAs (i.e., functional RNAs synthesized by in vitro selection technique), by applying the spectral graph partitioning technique. Our analysis shows that the majority of synthetic RNAs possess between two to six vertices and their second eigenvalues lie between one and two. In contrast, natural RNA structures mostly have nine or ten vertices and are less compact with the second eigenvalue below unity. Our statistical analysis (at 95 percentile) also reveals three criteria important for designing novel functional RNAs. Firstly, RNA sequences screened from a large random library, with length of 80 nucleotides and 32.31% paired bases, are very likely to fold into functional RNAs. Secondly, their predicted structures should possess two to six vertices inclusively. Thirdly, to minimize the number of false positives, a combination of filtering parameters should be included, the percentage G/C content of 65.95% and the normalized minimum free energy of -0.021 kcal/mol per nucleotide.


Minimum Free Energy Laplacian Matrix Internal Loop Hairpin Loop Hammerhead Ribozyme 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Stanley NG Kwang Loong
    • 1
    • 2
  • Santosh K. Mishra
    • 1
    • 2
  1. 1.NUS Graduate School for Integrative Sciences & EngineeringNational University of SingaporeSingapore
  2. 2.Agency for Science, Technology and Research, MatrixBioinformatics InstituteSingapore

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