Tracy Neilson

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Thermodynamic parameters for prediction of RNA duplex stability are reported. One parameter for duplex initiation and 10 parameters for helix propagation are derived from enthalpy and free-energy changes for helix formation by 45 RNA oligonucleotide duplexes. The oligomer sequences were chosen to maximize reliability of secondary structure predictions. Each(More)
The Mars Exploration Rover “Spirit” suffered a debilitating anomaly that prevented communication with Earth for several anxious days. With the eyes of the world upon us, the anomaly team used each scrap of information, our knowledge of the system, and sheer determination to analyze and fix the problem, then return the vehicle to normal operation. This paper(More)
The role of stacking in terminal base-pair formation was studied by comparison of the stability increments for dangling ends to those for fully formed base pairs. Thermodynamic parameters were measured spectrophotometrically for helix formation of the hexanucleotides AGGCCUp, UGGCCAp, CGGCCGp, GCCGGCp, and UCCGGAp and for the corresponding pentanucleotides(More)
The stabilizing effects of dangling ends and terminal base pairs on the core helix GCGC are reported. Enthalpy and entropy changes of helix formation were measured spectrophotometrically for AGCGCU, UGCGCA, GGCGCCp, CGCGCGp, and the corresponding pentamers XGCGCp and GCGCYp containing the GCGC core plus a dangling end. Each 5' dangling end increases helix(More)
In order to make efficient use of T4 RNA ligase in a program involving chemical-enzymatic oligoribonucleotide synthesis, the sequence effects of the acceptor oligomer have been refined. The reaction of the donor molecules pCp and pUpUpUpCp with a series of trinucleoside diphosphates ApApN, CpNpA and NpCpA (where N = U, C, A or G) was examined.(More)
A set of parameters, devised for the prediction of 1H NMR chemical shifts of heterobase and anomeric protons in the high temperature (greater than 70 degrees C) spectra of RNA oligomers has been found to be applicable to the corresponding DNA oligomers. Fifteen examples of DNA oligomers that have had high temperature spectra recorded and assigned show a(More)
Thermodynamic parameters of helix formation are reported for seven oligoribonucleotides containing only G.C pairs. These data are used with the nearest-neighbor model to calculate enthalpies and free energies of base-pair formation for G.C pairs. For helix initiation, the free energy change at 37 degrees C, delta G(0)37, is +3.9 kcal/mol; for helix(More)
Thermodynamic parameters of helix formation were measured spectroscopically for seven hexaribonucleotides containing a GC tetramer core and G.U or other terminal mismatches. The free energies of helix formation are compared with those for the tetramer core alone and with those for the hexamer with six Watson-Crick base pairs. In 1 M NaCl, at 37 degrees C,(More)