Highlights of the IMA workshop RNA in Biology, Bioengineering, and Biotechnology are summarized, including recent developments in RNA secondary structure prediction and RNA design, innovative mathematical constructs for RNA structure, bioinformatics advances in RNA structure analysis and prediction, and experimental progress in RNA folding and imaging. In small things considered is the world re...

RNA structure plays a crucial role in gene maturation, regulation and function. Determining the form and frequency of RNA folds is essential for a better understanding of how RNA exerts its functions. Low-throughput studies have focused on RNA primary sequences and expression levels, but with an emphasis on relatively small numbers of transcripts. However, with the recent advent of high-through...

RNA was first explored and understood as a messenger molecule, relaying DNA encodings of amino acids during protein synthesis. Beyond messenger RNA, however, a class of RNA known as non-coding RNA plays fundamental roles in transcriptional and translational gene regulation. As the biological mantra goes, form fits function, and these regulatory roles depend on the 3-D structure of the RNA molec...

Subgenomic (sg) mRNAs are small viral messages that are synthesized by polycistronic positive-strand RNA viruses to allow for the translation of certain viral proteins. Tombusviruses synthesize two such sg mRNAs via a premature termination mechanism. This transcriptional process involves the viral RNA-dependent RNA polymerase terminating minus-strand RNA synthesis prematurely at internal RNA si...

Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces the research on the structure and functional interactions of these RNA gene sequences. We mine the evolutionary sequence record to derive precise information about the function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability mode...

Satellite tobacco mosaic virus (STMV) is a T = 1 icosahedral virus with a single-stranded RNA genome. It is widely accepted that the RNA genome plays an important structural role during assembly of the STMV virion. While the encapsidated form of the RNA has been extensively studied, less is known about the structure of the free RNA, aside from a purported tRNA-like structure at the 3' end. Here...

objective: rna interference (rnai) is the most potent technique for gene silencing in eukaryotic cellular system at transcriptomic level. genetic disorders and cancers are important targets for therapeutic development of this technique. in order to bypass the temporary dpwnregulation by sirna, a new generation of shrna named shrnamir has developed. silencing construct with structure similar to ...

RADAR is a web server that provides a multitude of functionality for RNA data analysis and research. It can align structure-annotated RNA sequences so that both sequence and structure information are taken into consideration during the alignment process. This server is capable of performing pairwise structure alignment, multiple structure alignment, database search and clustering. In addition, ...