Pluripotency, the ability of a cell to give rise to all of the cells of an organism, is a fascinating and mysterious characteristic of embryonic stem (ES) cells. Recent extensive molecular studies of mouse ES cells have revealed the roles played by transcription factor networks and epigenetic processes in the maintenance of ES cell pluripotency (Niwa 2007). However, no direct evidence to connec...

An alternative protocol (PROT31) for 3C has been adopted by the author's lab. Much of it is identical to this version. The major differences are in the amounts of DNA used at different steps. We reliably get the same results as with this version, but also a greater yield of 3C material. Yields from this version are ample for real-time PCR analysis, but greater yields are required if the 3C mate...

Although the art of predicting molecular conformation has not yet reached maturity, it is no longer in its infancy. On the one hand, model-building techniques taking account of van der Waals’ radii and hydrogen bonding have been used to interpret ambiguous experimental data, leading Pauling & Corey to the a-helix and B-pleated sheet, and Watson & Crick to the double helix of DNA. On the other h...

Abstract We consider the problem of recovering three-dimensional atomic structure a flexible macromolecule from heterogeneous cryogenic electron microscopy (cryo-EM) dataset. The dataset contains noisy tomographic projections electrostatic potential macromolecule, taken different viewing directions, and in case, each cryo-EM image corresponds to conformation macromolecule. Under assumption that...

Pre-miR-675 is a microRNA expressed from the exon 1 of H19 long noncoding RNA, and atypical expression pre-miR-675 has been linked with several diseases disorders including cancer. To execute its function inside cell, folded into particular conformation, which aids in interaction other biological molecules. However, exact folding dynamics protein-binding motifs are currently unknown. Moreover, ...

The conformational states of Escherichia coli Rep helicase undergoing ATP hydrolysis while bound to a partial-duplex DNA (pdDNA) were studied using single-molecule FRET. Crystallographic studies showed that Rep bound to single-stranded DNA can exist in open and closed conformations that differ in the orientation of the 2B subdomain. FRET measurements between eight Rep mutants donor-labeled at d...