Advanced Design of Structural RNAs Using RNARedPrint.

Abstract

RNA design addresses the need to build novel RNAs, e.g., for biotechnological applications in synthetic biology, equipped with desired functional properties. This chapter describes how to use the software RNARedPrint for the de novo rational design of RNA sequences adopting one or several desired secondary structures. Depending on the application, these structures could represent alternate configurations or kinetic pathways. The software makes such design convenient and sufficiently fast for practical routine, where it even overcomes notorious problems in the application of RNA design, e.g., it maintains realistic GC content.