WRAP53 Is Essential for Cajal Body Formation and for Targeting the Survival of Motor Neuron Complex to Cajal Bodies

The WRAP53 protein regulates the formation and maintenance of Cajal bodies (nuclear sub-organelles), as well as directs the recruitment of nuclear factors to Cajal bodies

Comparisons between Chemical Mapping and Binding to Isoenergetic Oligonucleotide Microarrays Reveal Unexpected Patterns of Binding to the Bacillus subtilis RNase P RNA Specificity Domain†

ABSTRACT: Microarrays with isoenergetic pentamer and hexamer 20-O-methyl oligonucleotide probes with LNA (locked nucleic acid) and 2,6-diaminopurine substitutions were used to probe the binding sites on theRNase P RNA specificity domain of Bacillus subtilis. Unexpected binding patterns were revealed. Because of their enhanced binding free energies, isoenergetic probes can break short duplexes, merge adjacent loops, and/or induce refolding. This suggests new approaches to the rational design of short oligonucleotide therapeutics but limits the utility of microarrays for providing constraints for RNA structure determination. The microarray results are compared to results from chemical mapping experiments, which do provide constraints. Results from both types of experiments indicate that the RNase P RNA folds similarly in 1MNaþ and 10 mMMg2þ. Binding of RNA to RNA is important for many natural func-tions, includingproteinsynthesis (1,2), translationregulation (3,4), gene silencing (5, 6), metabolic regulation (7), RNAmodification (8, 9), etc. (10-13). Binding of oligonucleotides toRNAs is impor-tant for therapeutic approaches, such as siRNA, ribozymes, and antisense therapy (14, 15).Much remains to bediscovered, however, of the rules for predicting binding sites andpotential therapeutics