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. To test end or base composition effects, new sets of duplexes are included that have identical nearest neighbors, but different base compositions and therefore different ends. Duplexes with terminal GC pairs are more stable than duplexes with the same nearest neighbors but terminal AU pairs. Penalizing terminal AU base pairs by 0.45 kcal/mol relative to terminal GC base pairs significantly improves predictions of ∆G°3 7 from a nearest-neighbor model. A physical model is suggested in which the differential treatment of AU and GC ends accounts for the dependence of the total number of Watson-Crick hydrogen bonds on the base composition of a duplex. On average, the new parameters predict ∆G°3 7 , ∆H°, ∆S°, and T M within 3.2%, 6.0%, 6.8%, and 1.3°C, respectively. These predictions are within the limit of the model, based on experimental results for duplexes predicted to have identical thermodynamic parameters.The thermodynamics of secondary structure formation are important for unraveling structure-function relationships for RNA. For example, these thermodynamics provide a foundation for predicting secondary structure and stability, both of which can correlate with function. Moreover, predicting secondary structure is a crucial intermediate step toward predicting three-dimensional structure (1, 2). In addition, differences between the thermodynamics of secondary structure formation and of overall folding can provide insight into the thermodynamics of tertiary structure formation (3-7).Watson-Crick base pairs are one of the most important motifs in RNA secondary structures. The thermodynamics of Watson-Crick base pair formation have been studied in short RNA duplexes (8, 9). The results are well-represented by a nearest-neighbor model in which the thermodynamic stability of a base pair is dependent on the identity of the adjacent base pairs. This model has been termed an individual nearest-neighbor (INN) model (10, 11). The pioneering implementation by Borer et al. (8) employed 6 nearest-neighbor parameters and separate initiation parameters for duplexes with and without a GC base pair. Due to advances in oligoribonucleotide synthesis (12), Freier et al. (9) were able to determine all 10 nearest-neighbor parameters in the INN model and the initiation parameter for duplexes with at least one GC base pair. The initiation parameter for duplexes with only AU base pairs was not determined.It has been suggested that a nearest-neighbor model that treats terminal base pairs differently from internal base pairs (8) or treats terminal GC base pairs differently from terminal AU base pairs (10, 11, 13) may improve modeling of duplex stability. The model proposed by Gray (10) has been termed an independent short sequence (ISS) model because the 14 sequence-dependent parameters of the model must be combined into 12 "short sequence" p...

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The blockbuster chemotherapy drug paclitaxel is widely presumed to cause cell death in tumors as a consequence of mitotic arrest, as it does at concentrations routinely used in cell culture. However, we determine here that paclitaxel levels in primary breast tumors are well below those required to elicit sustained mitotic arrest. Instead, cells in these lower concentrations of drug proceed through mitosis without substantial delay and divide their chromosomes on multipolar spindles, resulting in chromosome missegregation and cell death. Consistent with these cell culture data, the majority of mitotic cells in primary human breast cancers contain multipolar spindles after paclitaxel treatment. Contrary to the previous hypothesis, we find that mitotic arrest is dispensable for tumor regression in patients. These results demonstrate that mitotic arrest is not responsible for the efficacy of paclitaxel, which occurs due to chromosome missegregation on highly abnormal, multipolar spindles. This mechanistic insight may be used to improve selection of future anti-mitotic drugs and to identify a biomarker with which to select patients likely to benefit from paclitaxel.