Ribbon channel plate rotating drum DNA sequencing device.

A new design DNA sequencing electrophoresis device is described. The device, called the ribbon channeled plate rotating drum (rprd), consists of two major components, the plate assembly and the drum assembly. The plate assembly contains a machined or etched plate of individual micro-channels called the ribbon channeled plate. The ribbon channeled plate and other components of the plate assembly combine the advantages of thin gels and capillary arrays in a single unit with few of the disadvantages. The other major component of rprd is the drum assembly, which facilitates direct blotting onto deposition membranes affixed to a large plastic drum. The drum with attached membrane and deposited electrophoretically resolved ladders is easily moved to special units facilitating downstream processing and detection. The drum unit, although versatile, is specifically designed to be used with multiplex sequencing.

Gene synthesis and functional expression of a protein exhibiting monodomain IgG Fc binding.

A gene encoding a bacterial IgG Fc binding domain was designed and synthesized. The synthetic DNA fragment was cloned 3' to an inducible trpE promoter such that expression of the gene in Escherichia coli produced abundant Fc binding protein fused to the first seven amino acids of the trpE protein. The recombinant protein contained a single Fc binding domain and demonstrated efficient binding to human IgG in Western blot analysis. This protein degraded rapidly following cell lysis in the absence of protease inhibitors, but could be effectively protected by the addition of protease inhibitor. After purification of the protein by IgG affinity chromatography, IgG Fc binding ability was retained for at least 24 h at either 23 or 37 degrees C and on heating for 15 min at temperatures up to 65 degrees C. No immunoprecipitation was observed in interactions between the monodomain Fc binding protein and IgG molecules. Unlike staphylococcal protein A, no detectable binding of the monodomain IgG Fc binding protein was observed to either IgM or IgA. Truncated proteins, expressed from a series of 3' deletions of the synthetic gene, were used to estimate the minimum portion of a monodomain Fc binding protein that retained Fc binding ability.

Protein expression from an Escherichia coli/Bacillus subtilis multifunctional shuttle plasmid with synthetic promoter sequences.

A plasmid shuttle vector (pSP10) was designed and constructed to simplify screening of cloned DNA and to facilitate expression of the protein products. The plasmid contained the following features: (i) a selection gene, chloramphenicol acetyltransferase; (ii) an indicator gene encoding beta-galactosidase for visual identification of colonies containing DNA inserts; (iii) a cloning region immediately upstream from the indicator gene; (iv) origins of replication recognized by both Escherichia coli and Bacillus subtilis; and (v) a synthetic DNA expression control sequence, including -35 and -10 regions, ribosomal binding site, and transcriptional and translational start sites. The promoter region is a synthetic consensus sequence derived from published B. subtilis promoters. The plasmid has been shown to replicate actively in E. coli and B. subtilis and to confer chloramphenicol resistance to both hosts. DNA inserted at the cloning region inactivates the indicator gene, resulting in white colonies on 5'-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside plates. beta-Galactosidase has been expressed from pSP10 in both E. coli and B. subtilis. A comparison was made of the expression levels of beta-galactosidase from the same plasmid which had been modified to contain: (i) the synthetic control region, (ii) no promoter region, (iii) the synthetic control region cloned in the opposite orientation, or (iv) the tac promoter.

Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure.

The conditional probability, P(sigma/x), is a statement of the probability that the value of sigma will be found given the prior information that a value of x has been observed. Here sigma represents any one of the secondary structure types, alpha, beta, tau, and rho for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N-cap and C-cap values; (4) Chou-Fasman conformational parameters for helix, P alpha, for sheet, P beta, and for turn, P tau; and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, I alpha, for sheet, I beta, for turn, I tau, and for random structure, I rho. Plots of P(sigma/x) vs. x are demonstrated to provide information about the correlation between structure and attribute, sigma and x. The separations between different P(sigma/x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P(alpha/x), P(beta/x), P(tau/x) and P(rho/x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix greater than P alpha much greater than N-cap greater than C-cap approximately I alpha approximately I tau. The information value for turns, I tau, was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: I beta much greater than P beta approximately hydropathy greater than I rho approximately hydrophobic moment assuming sheet. Three attributes, at their low values, were found to give significant discrimination for the absence of helix: I alpha approximately P alpha approximately hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: P beta much greater than I rho approximately hydropathy. Indications of the absence of sigma could be as useful for some applications as the indication of the presence of sigma.

Color graphics representations of large sequences in the GEM environment.

The analytical and descriptive color graphics capabilities (the GEM environment) of the CAGE/GEM(a) software system are described using bacteriophage lambda (48,502 base pairs) and Epstein Barr virus (172,282 base pairs) as examples. Genetics and features, as graphic drawings, and the results of sequence analysis as pseudo-colored representations, are simultaneously displayed at all zooming levels. The present upper limit on sequence size is 5 x 10(5) bases. The overlay editor utility which provides the capability to structure complex sequence associated data and knowledge bases into a manageable color graphics format is also described. Holistic correlations that can be made by the display of bacteriophage lambda and Epstein Barr virus in the GEM environment are also discussed.

Cloning simulation in the cage environment.

The CAGE/GEM(TM) software toolkit for genetic engineering is briefly described. The system functionally uses color graphics and is menu driven. It integrates genetics and features information ("Overlays") with information based on sequence analysis ("Representations"). The system is structured around CAD (Computer Aided Design) principles. The CAGE (Computer Aided Genetic Engineering) aspects of the software are emphasized and illustrated by a simulated cloning of the hepatitis B core antigen gene into the BAMHI site of plasmid pBR322.

Events in the evolution of pre-proinsulin.

An extensive computer-assisted analysis of known pre-proinsulin coding sequences has shown correlations that can be interpreted as evidence for an intron-mediated juxtaposition of exons in the evolution of these genes. The evidence includes the discovery that the regions of the pre-proinsulin genes that code for the signal peptide consist of nearly tandem repeating units of nine base pairs. This pattern reappears in the C region of the genes after a large intron that occurs in three of the four genes analyzed. A model is proposed in which primordial insulin was coded for by two separate minigenes arising from a gene duplication, each with identical or nearly identical signal peptide coding regions. The minigenes fused into one transcriptional unit mediated by the large intron, and the signal peptide coding region of one of the putative minigenes evolved into the latter portion of the C peptide coding region.

Interferon induction and macrophage activation by a mycovirus double-stranded RNA/tobramycin complex following treatment with human serum.

Double-stranded RNA (dsRNA) molecules, generally effective inducers of interferon (IFN), have a weak potency in man apparently because of the presence of a serum RNAase which quickly inactivates extracellular dsRNA. We have discovered that tobramycin, an aminoglycoside, protects Penicillium chrysogenum mycovirus dsRNA (PCMdsRNA) from the degradative action of the nuclease. Exposure of the dsRNA/tobramycin complex to human serum results in some degradation, but still permits the production of significantly high titers of IFN upon injection into mice. Intraperitoneal (i.p.) treatment of CFI mice with both dsRNA and dsRNA/tobramycin complex activated macrophages to inhibit the growth of P815 mastocytoma target cells. Following in vitro treatment with human serum, free dsRNA failed to activate peritoneal macrophages in vivo under conditions where this activity of dsRNA/tobramycin complex was retained. By varying the ratio of moles of tobramycin (as free base) to the moles of RNA phosphorous, toxicity can be minimized, while retaining the biologic activities of dsRNA.

Denaturation and renaturation of Penicillium chrysogenum mycophage double-stranded ribonucleic acid in tetraalkylammonium salt solutions.

The base composition dependence of double-stranded ribonucleic acid (RNA) melting was studied by observing the structure and widths of melting transitions for Penicillium chrysogenum mycophage RNA as well as differences in melting temperatures of two RNAs of different base composition. Double-stranded RNA melting is independent of base compositions in 3.5 M Et4NCl and 4.6 M Me4NCl, where the melting temperatures are 25 and 92 degrees C, respectively. Double-stranded RNA renaturation rate constants are reported in Et4NCl solutions. The nucleation rate constant is about 10 times lower than that for double-stranded deoxyribonucleic acid. Analyses of renaturation kinetics results lead to the conclusion that each of the three similar but separable RNA segments of Penicillium chrysogenum mycophage is unique.

Ionic strength effects on the stability and conformation of Penicillium chrysogenum mycophage double stranded RNA.

The effect of [Na+] on the stability and conformation of penicillium chrysogenum mycophage dsRNA (PCMdsRNA) was investigated using CD and UV optical techniques. Thermal melting profiles reveal prominent fine structure attributed to at least four regions of structural dissimilarity. A constant increased thermal stability of the dsRNA compared to DNA of the same base composition was observed over a concentration range of 1.5 times 10- minus 4 M to 4.5 times 10- minus 2 M Na+. At low ionic strengths ([Na+] less than 10- minus 3 M) Tm becomes independent of further decrease in [Na+] unless the dsRNA is exposed to high concentrations of EDTA, suggesting the involvement to tightly bound divalent cation. At relatively high ionic strengths ([Na+] greater than 0.1 M) a postulated A leads to A' ... conformation change occurs.