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DNA carries more than the list of biochemical ingredients that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals, which determine the degree to which the long, threadlike molecule moves and how it responds to proteins and other molecules that control its processing and govern its packaging. The chemical composition of base pairs directs the spatial disposition and fluctuations of successive residues. The observed arrangements of these moieties in high-resolution protein–DNA crystal structures provide one of the best available estimates of the natural, sequence-dependent structure and deformability of the double-helical molecule. Here, we update the set of knowledge-based elastic potentials designed to describe the observed equilibrium structures and configurational fluctuations of the ten unique base-pair steps. The large number of currently available structures makes it possible to characterize the configurational preferences of the DNA base-pair steps within the context of their immediate neighbors, i.e., tetrameric context. Use of these knowledge-based potentials shows promise in accounting for known effects of sequence in long chain molecules, e.g., the degree of curvature reported in classic gel mobility studies and the recently reported sequence-dependent responses of supercoiled minicircles to nuclease cleavage.more » « less
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null (Ed.)Polymeric membranes for separation of pharmaceutical intermediates/products by organic solvent nanofiltration (OSN) have to be highly resistant to many organic solvents including high-boiling polar aprotic ones, e.g., N- methyl-2-pyrollidone (NMP), dimethylsulfoxide (DMSO), dimethylformamide (DMF). Unless cross-linked, few polymers resist swelling or dissolution in such solvents; however particular perfluoropolymers are resistant to almost all solvents except perfluorosolvents. One such polymer, designated AHP1, a glassy amorphous hydrophobic perfluorinated polymer, has been studied here. Additional perfluoropolymers studied here are hydrophilically modified (HMP2 and HMP3) versions to enhance the flux of polar aprotic solvents. OSN performances of three types of membranes including the hydrophilically modified ones were studied via solvent flux and solute rejection at pressures up to 5000 kPa. The solutes were four active pharmaceutical ingredients (APIs) or pharmaceutical intermediates having molecular weights (MWs) between 432 and 809 Da and three dyes, Oil Blue N (378 Da), Sudan Black B (456 Da), Brilliant Blue R (826 Da). Solvents used were: ethyl acetate, toluene, n- heptane, iso-octane, DMSO, tetrahydrofuran (THF), DMF, acetone, NMP, methanol. Test cells included stirred cells and tangential flow cells. Pure solvent fluxes through three membrane types were characterized using a particular parameter employing various solvent properties. All three membranes achieved high solute rejections around 91–98% at ambient temperatures. HMP2 membrane achieved 95% solute rejection for an API (809 Da) in DMSO at a high temperature, 75 ◦C. A two-stage simulated nanofiltration process achieved 99%+ rejection of a pharmaceutical intermediate (MW, 432 Da) in 75v% NMP-25v% ethyl acetate solution.more » « less
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