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

is the full version. It is available from www.cs.ucdavis.edu/~rogaway/umac/ UMAC: Fast and Secure Message Authentication

Abstract. We describe a message authentication algorithm, UMAC, which can authenticate messages (in software, on contemporary machines) roughly an order of magnitude faster than current practice (e.g., HMAC-SHA1), and about twice as fast as times previously reported for the universal hash-function family MMH. To achieve such speeds, UMAC uses a new universal hash-function family, NH, and a design which allows effective exploitation of SIMD parallelism. The “cryptographic ” work of UMAC is done using standard primitives of the user’s choice, such as a block cipher or cryptographic hash function; no new heuristic primitives are developed here. Instead, the security of UMAC is rigorously proven, in the sense of giving exact and quantitatively strong results which demonstrate an inability to forge UMAC-authenticated messages assuming an inability to break the underlying cryptographic primitive. Unlike conventional, inherently serial MACs, UMAC is parallelizable, and will have ever-faster implementation speeds as machines offer up increasing amounts of parallelism. We envision UMAC as a practical algorithm for next-generation message authentication.