Publications - Published papers
Please find below publications of our group. Currently, we list 565 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking in vitro
Kirsch, Rebecca and Olzog, Vanessa Janett and Bonin, Sonja and Weinberg, Christina E and Betat, Heike and Stadler, Peter F and Mörl, Mario
Download
Status: Published
BioTechniques 67: 178-183
Abstract
Until recently, RNA–RNA interactions were mainly identified by crosslinking RNAs with interacting proteins, RNA proximity ligation and deep sequencing. Recently, AMT-based direct RNA crosslinking was established. Yet, several steps of these procedures are rather inefficient, reducing the output of identified interaction partners. To increase the local concentration of RNA ends, interacting RNAs are often fragmented. However, the resulting 2′,3′-cyclic phosphate and 5′-OH ends are not accepted by T4 RNA ligase and have to be converted to 3′-OH and 5′-phosphate ends. Using an artificial mRNA/sRNA pair, we optimized the workflow downstream of the crosslinking reaction in vitro. The use of a tRNA ligase allows direct fusion of 2′,3′-cyclic phosphate and 5′-OH RNA ends.