The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces),the server circumvents the problem of portability of this software. Detailed output,in the form of structure plots with or without reliability information,single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information,but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/ mfold. This URL will be referred to as ‘MFOLDROOT’.

/pdf/mfold-web-server-for-nucleic-acid-folding-and-hybridization-3pzoe1h05m.pdf

Mfold web server for nucleic acid folding and hybridization prediction

A procedure for the isolation of deoxyribonucleic acid from micro-organisms

http://www.protocol-online.org/forums/index.php?app=core&module=attach&section=attach&attach_id=2894

Studies on transformation of Escherichia coli with plasmids

3.2.3. Hydroformylation 2467 3.2.4. Dimerization 2468 3.2.5. Oxidative Cleavage and Ozonolysis 2469 3.2.6. Metathesis 2470 4. Terpenes 2472 4.1. Pinene 2472 4.1.1. Isomerization: R-Pinene 2472 4.1.2. Epoxidation of R-Pinene 2475 4.1.3. Isomerization of R-Pinene Oxide 2477 4.1.4. Hydration of R-Pinene: R-Terpineol 2478 4.1.5. Dehydroisomerization 2479 4.2. Limonene 2480 4.2.1. Isomerization 2480 4.2.2. Epoxidation: Limonene Oxide 2480 4.2.3. Isomerization of Limonene Oxide 2481 4.2.4. Dehydroisomerization of Limonene and Terpenes To Produce Cymene 2481

Chemical Routes for the Transformation of Biomass into Chemicals

High-performance liquid chromatography is a promising alternative for determining the G+C content of bacterial deoxyribonucleic acid (DNA). The method which we evaluated involves enzymatic degradation of the DNA to nucleosides by P1 nuclease and bovine intestinal mucosa alkaline phosphatase, separation of the nucleosides by high-performance liquid chromatography, and calculation of the G+C content from the apparent ratios of deoxyguanosine and thymidine. Because the nucleosides are released from the DNA at different rates, incomplete degradation produces large errors in the apparent G+C content. For partially purified DNA, salts are a major source of interference in degradation. However, when the salts are carefully removed, the preparation and degradation of DNA contribute little error to the determination of G+C content. This method also requires careful selection of the chromatographic conditions to ensure separation of the major nucleosides from the nucleosides of modified bases and precise control of the flow rates. Both of these conditions are achievable with standard equipment and C18 reversed-phase columns. Then the method is precise, and the relative standard deviations of replicate measurements are close to 0.1%. It is also rapid, and a single measurement requires about 15 min. It requires small amounts of sample, and the G+C content can be determined from DNA isolated from a single bacterial colony. It is not affected by contamination with ribonucleic acid. Because this method yields a direct measurement, it may also be more accurate than indirect methods, such as the buoyant density and thermal denaturation methods. In addition, for highly purified DNA, the extent of modification can be determined.

Precise Measurement of the G+C Content of Deoxyribonucleic Acid by High-Performance Liquid Chromatography

When DNA is irradiated in solution with UV light at 254 m mu , loss of transforming activity and changes in the physical chemical properties of the DNA can be detected The loss of biological activity, studied with DNA isolated from D pneumoniae and B subtilis, depends on the genetic marker under investigation as well as on its size and on the molecular weight of the DNA being irradiated When exposed to higher dose levels, native DNA is both partially degraded and weakened in structure Cross-linking of the complementary strands has been detected The UV induced physical chemical alterations have been detected by the lowering of the denaturation temperature, a drop in sedimentation coefficient after denaturation, a decrease in viscosity, an increase in buoyant density in a CsCl gradient, a cross-linking of DNA strands and an increase in the pH at which the molecules denature Most of the physical chemical changes are accentuated by a higher adenine plus thymine content of the DNA and by the substitution of 5bromouracil for thymine Denatured and native DNA behave differently when exposed to the same dose at the same wavelength As in the biological experiments, for the same dose levels, the smaller themore » molecular weight of the DNA, the less the physical chemical damage Both the biological and the viscosity changes induced by UV show no oxygen effect The photoreactivating enzyme from bakers' yeast reactivates UV-treated transforming DNA in the presence of visible light; the reactivation might be due in part to the disruption of the cross-links induced by UV« less

The effects of ultraviolet light on the biological and physical chemical properties of deoxyribonucleic acids.

A Conformation Examination of Poly-L-alanine and Poly-D,L-alanine in Aqueous Solution

Towards a total macromolecular analysis of sea urchin embryo chromatin

Self-complementary oligoribonucleotides: effects of helix defects and guanylic acid-cytidylic acid base pairs.

Fifty-four kilobase pairs (kbp) of cloned chicken DNA containing the entire 38-kbp pro alpha 2 (I) collagen gene have been isolated and characterized. DNA sequence analysis of a select 4 kbp of the gene has precisely described 14 exons which comprise one-third of the sequences encoding the triple-helical domain of the collagen protein. These exons range in size from 45 to 108 base pairs (bp), are all multiples of the 9 bp that code for the repeating triplet, Gly-X-Y, and have an average size of 70 bp. About 50 introns interrupt this gene. Nevertheless, introns do not separate the coding sequences for the ends of the central triple-helical structural domain and the ends of the propeptide domains.

Paul Doty

Papers

The effects of ultraviolet light on the biological and physical chemical properties of deoxyribonucleic acids.

A Conformation Examination of Poly-L-alanine and Poly-D,L-alanine in Aqueous Solution

Towards a total macromolecular analysis of sea urchin embryo chromatin

Self-complementary oligoribonucleotides: effects of helix defects and guanylic acid-cytidylic acid base pairs.

Structure of the pro alpha 2 (I) collagen gene.