Loops are abundant in native RNA structures and proliferate close to the unfolding transition. By including a statistical weight approximately l(-c) for loops of length l in the recursion relation for the partition function, we show that the heat capacity depends sensitively on the presence and value of the exponent c, even for a short explicit tRNA sequence. For long homo-RNA, we analytically ...

Group I introns constitute excellent systems for analyzing the relationship between RNA tertiary folding and catalysis. Within a hierarchical framework interpretation of RNA folding, secondary structure motifs subtend RNA three-dimensional (3D) architecture. Thus, mutations in two-dimensional motifs are expected to have effects different from those disrupting 3D contacts. Using UV spectroscopy,...

Fluorescence techniques are commonly and powerfully applied to monitor biomolecular folding. In a limited fashion, the fluorescence emission intensity of covalently attached pyrene has been used as a reporter of RNA conformational changes. Here, we pursue two goals: we examine the relationship between tether identity and fluorescence response, and we determine the general utility of pyrene fluo...

Background The most common genetic cause of Frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS) is an intronic GGGGCC hexanucleotide repeat expansion in C9orf72 (C9FTD/ALS). Transcribed RNAs sequester RNA-binding proteins (RBPs) into nuclear cytoplasmic foci, which inhibits their normal functions. also support translation toxic peptides through a process known as associated no...

Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates' secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the R...

The functions of RNA molecules are defined by their spatial structure, whose folding is regulated by numerous factors making RNA very similar to proteins. Prediction of RNA folding nuclei gives the possibility to take a fresh look at the problems of the multiple folding pathways of RNA molecules and RNA stability. The algorithm previously developed for prediction of protein folding nuclei has b...

Fluorescence-detected stopped-flow and equilibrium methods have been used to study the mechanism for binding of pyrene (pyr)-labeled RNA oligomer substrates to the ribozyme (catalytic RNA) from Tetrahymena thermophila. The fluorescence of these substrates increases up to 25-fold on binding to the ribozyme. Stopped-flow experiments provide evidence that pyr experiences at least three different m...

Transitions between different conformational states, so-called conformational switching, are intrinsic to RNA catalytic and regulatory functions. Often, conformational switching occurs on time scales of several seconds. In combination with the recent real-time NMR experiments (Wenter et al. Angew. Chem. Int. Ed. 2005, 44, 2600; Wenter et al. ChemBioChem 2006, 7, 417) for the transitions between...

A wealth of information on RNA folding and ribonucleoprotein assembly has emerged from analyses of structures and from the use of innovative biophysical tools. Although integrating data obtained from static structures with dynamic measurements presents major challenges, such efforts are opening new vistas on the RNA folding landscape.

RNA folding in the cell occurs during transcription. Expedient RNA folding must avoid the formation of undesirable structures as the nascent RNA emerges from the RNA polymerase. We show that efficient folding during transcription of three conserved noncoding RNAs from Escherichia coli, RNase P RNA, signal-recognition particle RNA, and tmRNA is facilitated by their cognate polymerase pausing at ...