Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination

davidd submitted, created time 8 months 4 weeks (www.cell.com)

Transcription termination by bacterial RNA polymerase (RNAP) occurs at sequences coding for a GC-rich RNA hairpin followed by a U-rich tract. They used single-molecule techniques to investigate the mechanism by which three representative terminators (his, t500, and tR2) destabilize the elongation complex (EC). And they propose a quantitative, energetic model that predicts the behavior for these terminators and mutant variants.

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High-resolution design of a protein loop

davis submitted, created time 1 year 2 months (www.pnas.org)

Despite having irregular structure, protein loops often adopt specific conformations that are critical to protein function. Most studies in de novo protein design have focused on creating proteins with regular elements of secondary structure connected by very short loops or turns.

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A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

psychologist submitted, created time 1 year 6 months (nar.oxfordjournals.org)

We propose a new model for predicting the retention time of oligonucleotides. The model is based on {nu} support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data.

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