The Wonderful World of RNA DNA RNA protein

The Wonderful World of RNA DNA RNA protein

Complexity of RNA Folding • 1 strand • 4 building blocks • Basic structural element: double helix RNA folds back and forms • Non-Watson Crick base pairs • base triples • Loop–loop, -single strand, -helix, helix - helix interactions The shape of an RNA molecule determines its function

RNA Base Pairs G G C U A G G A U A

I. RNA tetraloops Abundant in Nature Fullfill many structural and functional roles 16 S r. RNA: Of all loops > 50% are tetraloops Most are UNCG or GNRA Tetrahymena ribozyme

II. Cis-regulating elements of poliovirus Single stranded RNA genome 7440 nt

Poliovirus 5’-UTR Poliovirus 5´-UTR cloverleaf structure Aim: To characterize the stem-loop D - 3 CD interaction by using in vivo SELEX.

In vivo selection of randomly generated mutants polio wild type sequence N N N-N U-A G-C random pool of 48 = 65536 possible sequences GC U G U-G A-U U-A G-C In vivo production of virus mutants N N N-N U-A G-C 22 different selected sequences

Structures of UNCG and GNRA loops differ A C A A U G A G C anti G anti syn U anti G G Du et al. , 2003 A Heus and Pardi, 1991

II. RNA pseudoknots • Occur in virtually all classes of RNA • Role in biological processes: - replication initiation - translational control - ribosomal frameshifting - core formation in larger RNAs

RNA pseudoknot formation

Ribosomal frameshifting SRV-1 genome overlapping region

NMR-derived structure of SRV-1 RNA pseudoknot

Guanine Riboswitch G ON Guanine absent OFF Guanine present Guanine

Structural Differences P 2 -P 3 interaction in both the free form and complex P 3 arm P 2 arm Disordered base pairs in free aptamer Base pairs in free form and complex Flexible 5 -residue “lid” P 1 arm

Importance for riboswitching