Spectral graph partitioning analysis of in vitro synthesized RNA structural folding

Authors:
Stanley NG Kwang Loong;Santosh K. Mishra
Affiliations:
NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore;NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore
Venue:
PRIB'06 Proceedings of the 2006 international conference on Pattern Recognition in Bioinformatics
Year:
2006

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Abstract

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.