19,20-based method to measure the hybridization kinetics in DNA and RNA duplexes21. Using this approach, we showed that m6A preferentially slows the apparent rate of RNA duplex annealing by ~5–10-fold while having little effect on the apparent rate of duplex melting21(Fig.1...
While these models have proven to be effective when describing small-scale/ narrowly defined conformational transitions, the vast phase space associated with accommodation makes it computationally intractable to calculate the free energy. In contrast, through the use of simpler models, one may evaluate ...
The PM and MM probe of one probe pair are located physically next to each other on the microarray. Both MAS5 and dChip in the PMMM mode use this information to calculate gene expression. However, in the literature there is a debate over the usefulness of MM probes, which has resulted ...
It is possible to calculate the expected average fragment size for a given genomic DNA if the percent GC content of the DNA and the recognition sequence of the restriction enzyme are known. For example, in a genome with 50% GC content and no dinucleotide bias, a four-cutter can be expecte...
This was demonstrated by the simultaneous detection of the mutation underlying Miller syndrome by WGS of a family consisting of two affected siblings and their parents with the added bonus of being able to calculate a human intergenerational mutation rate of approximately 1.1 × 10-8 per position ...
This writeup attempts to answer to the question, "how much more (or less) likely am I to have COVID given a positive (or negative) test result?" In particular, this is an attempt to calculate theBayes factorfor different types of COVID test results. ...
such as the circumference of the arm (humerus) and leg (femur) bones, and compared them to dinosaurs; or they calculate the volume of three-dimensional reconstructions that approximate what the animal may have looked like in real life. Debate over which method is better has raged in the lite...
to their reproductive goals, encompassing individual, couple, and community perspectives. To ensure the health of the child they will raise, men are driven to maintain their own health. When considering couples, the importance of a healthy partnership in raising children may lead to the disclosure...
we used our simplified model to calculate the free energy of aa-tRNA elbow accommodation with EF-Tu bound to the ribosome in its post-hydrolysis, pre-Pi-release conformation21,29. Relative to the calculations described inFig. 1, the only difference in this set of simulations is that EF-Tu...
We next asked how it is possible that long-lived misfolded proteins are able to bypass the post-translational cellular chaperone machinery. To address this question we used coarse-grained Langevin dynamics to calculate the dissociation constant between the chaperone GroEL and three distinct conformational...