Identification of the mRNA start site is essential in establishing the full-length cDNA sequence of a gene and analyzing its promoter region, which regulates gene expression. Here we describe the development of a 5'-end serial analysis of gene expression (5' SAGE) that can be used to globally identify transcriptional start sites and the frequency of individual mRNAs. Of the 25,684 5' SAGE tags in the HEK293 human cell library, 19,893 matched to the human genome. Among 15,448 tags in one locus of the genome, 85.8%-96.1% of the 5' SAGE tags were assigned within -500 to +200 nt of mRNA start sites using the RefSeq, UniGene and DBTSS databases. This technique should facilitate 5'-end transcriptome analysis in a variety of cells and tissues.

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Using dissipative particle dynamics we model phase separation within block and grafted polymers composed of hydrophobic (A) and hydrophilic, acid-containing (C) beads. The grafted polymers have their hydrophilic beads located at the end of the grafted side chains. Pore morphologies are calculated at a hydration level l of 4 H 2 O molecules/C bead. Monte Carlo tracer diffusion calculations are used to model the restricted movement of water within the pore networks. For the block polymers we find that at fixed C bead fractions, or ion exchange capacity (IEC), an increase in C block length results in larger pores and increased water diffusion. For grafted polymers of equal IEC, increasing the side chain length results in a better connected pore network and increased long-range water mobility.

Using dissipative particle dynamics pore morphologies within model ionomer membranes are simulated. The ionomers are composed of hydrophobic backbones and side chains that are end-linked with a hydrophilic acid containing site. The separation distance between successive branching points is bi-modal, being alternating short (distance x) and long (distance y). The dependence of morphology on ion exchange capacity and separation distance is investigated. Phase separated morphologies were calculated at a water content of 16 vol. %. An increase of side chain density results in a decreasing size of the water containing pores, distance between them and decreasing Bragg spacing. For fixed side chain density, an increase in difference between the longer and shorter separation distance (y - x) results in a larger Bragg spacing. Monte Carlo calculations demonstrate that a large majority of the water is contained within a percolating network that allows for long-range diffusion. Diffusion constants vary drastically with architecture: Diffusion is fastest for architectures for which the side chains are highly non-uniformly distributed (y ≫ x). For architectures with the same side chain density, the tracer diffusion constants increase linearly with increase of the asymmetry ratio y∕x (y > x). This is caused by the cooperative action of those terminal acidic sites that are topologically close together, allowing them to arrange pair wise along the pore walls and make the pores larger. We verified that for polymer architectures that mimick Nafion1200 similar trends are obtained, resulting in increased H(2)O, O(2), and H(2) permeation for statistical side chain distribution as compared to a uniform distribution of side chains. This trend is most pronounced for H(2)O and less pronounced for H(2).

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