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Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.
TLDR
Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson-Crick base pairs, and on average, the new parameters predict DeltaG degrees37, DeltaH degrees, DeltaS degrees, and TM within the limit of the model. Expand
Improved free-energy parameters for predictions of RNA duplex stability.
TLDR
These parameters predict melting temperatures of most oligonucleotide duplexes within 5 degrees C, about as good as can be expected from the nearest-neighbor model. Expand
Structural Diversity of Triplet Repeat RNAs*♦
TLDR
The results of this study provide a comprehensive structural foundation for the functional analysis of triplet repeats in transcripts and demonstrate that the different susceptibility of various triplet repeat transcripts to serum nucleases can be explained by the sequence and structural features of the tested RNAs. Expand
Thermodynamics of single mismatches in RNA duplexes.
TLDR
The thermodynamic properties and structures of single mismatches in short RNA duplexes were studied in optical melting and imino proton NMR experiments and approximations are suggested for predicting stabilities of single mismatch stability. Expand
Exploring the energy landscape of a small RNA hairpin.
TLDR
An analysis of three variants shows that one of the intermediate RNA structures is a stacking-related trap affected by stem but not loop modification, while the other is an early intermediate that forms some stem and loop structure. Expand
Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods.
TLDR
Stopped-flow experiments provide evidence that pyr experiences at least three different microenvironments during the binding process, and a minimal mechanism is presented in which substrate initially base pairs to ribozyme and subsequently forms tertiary contacts in an RNA folding step. Expand
Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid.
TLDR
Comparison of the stability increments for terminal dangling ends and base pairs and of terminal GC and AU base pairs, indicates the free energy increment associated with forming a hydrogen bond can be about -1 kcal/mol of hydrogen bond. Expand
Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin.
TLDR
A strong context dependence for the free energy of hydrogen bond formation is suggested and the phylogenetic preference for GNRA (where N = A, C, G, or U and R = A or G) tetraloops may have a functional rather than thermodynamic basis. Expand
Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC.
TLDR
Optical melting experiments and laser temperature-jump experiments indicate the effect of Na+ concentration on the rate of duplex formation is much less than is observed for polynucleotides, consistent with expectations based on a counterion condensation model. Expand
The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes
TLDR
The influence of locked nucleic acid (LNA) residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes is reported and an equation is proposed to approximate the stabilities of complementary duplexes formed with RNA when at least one 2-methyl nucleotide separates LNA nucleotides. Expand
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