RNAstructure: software for RNA secondary structure prediction and analysis

<p>Abstract</p> <p>Background</p> <p>To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.</p> <p>Results</p> <p>RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.</p> <p>Conclusion</p> <p>The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at <url>http://rna.urmc.rochester.edu/RNAstructure.html</url>.</p

Two-dimensional NMR experiments for the assignment of aromatic side chains in 13C labeled proteins

As aromatic residues very often are part of the hydrophobic core of proteins, the unambiguous assignment of the aromatic proton resonances is essential for an accurate and precise structure determination. Instead of transferring1Hßcoherence to the aromatic protons via13C¿like in a number of published methods, in our new experiments the13C¿resonances are first correlated with the1Hßchemical shifts in one experiment and then with the aromatic proton resonances in four other experiments. Their short coherence transfer pathways make the experiments applicable to proteins with a molecular weight larger than 20 kDa, as is demonstrated forFusarium solani pisicutinase (214 residues). The dispersion of the C¿chemical shifts between different aromatic residue types is obvious, but even the dispersion within one type is sufficient to combine the experiments using only the C¿chemical shift and to assign nearly all aromatic proton resonances of cutinase. Author Keywords: heteronuclear NMR; resonance assignment; aromatic side chain; protein; cutinas