Development of RNA Stiffness Parameters and Analysis on Protein-RNA Binding Specificity: Comparison with DNA

Abstract

It has been well established that the elastic character of DNA plays an important role in protein-DNA binding specificity. In this work, we have analyzed the role of elasticity to understand the binding specificity of protein-RNA complexes. We have developed a sequence dependent stiffness scale for the trinucleotides in RNA and revealed the similarities and differences compared with DNA. We found that the stiffness of 15 trinucleotides has inverse effects and nine nucleotides are significantly different between RNA and DNA. The analysis on the relationship between RNA stiffness and RNA-binding specificity shows that the influence of elasticity is minimal in protein-RNA recognition, whereas it plays an important role in protein-DNA binding specificity. We observed a moderate correlation between stiffness and dissociation constant in U1A RBD1 protein and PP7 coat protein, whereas the correlation is poor for many other complexes. These results show that along with RNA stiffness, other interactions, such as shape complementarity, electrostatic interactions, hydrogen bonds and direct contacts between RNA and protein atoms are important for protein- RNA recognition. Keywords: Binding specificity, elasticity, protein-RNA recognition, stiffness, trinucleotides, protein-DNA, parameters, GLD-1, nucleotides, native gel electrophoresis