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

A stable histone core complex containing equimolar ratios of H2A, H2B, H3, and H4 has been isolated from chicken erythrocyte chromatin in high salt. This complex has been characterized by sedimentation and chemical cross-linking studies. In velocity ultracentrifugation, only one single sharp sedimentation boundary has been observed with sedimentation coefficient S020,w = 3.8 +/- 0.1. The molecular weight of the histone core complex has been investigated by low-speed sedimentation equilibrium studies over a wide range of protein concentration. Analysis of the apparent weight-average molecular weight as a function of concentration indicates that the histone core complex in 2 M NaCl, pH 9.0, is in equilibrium between a tetramer (H2A)(H2B)(H3)(H4) and an octamer [(H2A)(H2B)(H3)(H4)]2 species with a tetramer molecular weight of 55,000. The equilibrium constant K is approximately 1.2 X 10(-5) liter per mol at 10 degrees. Evidence of such a tetramer-octamer equilibrium in solution is also supported by the results of our chemical crosslinking experiments on the histone core complex.

https://www.pnas.org/content/pnas/75/4/1680.full.pdf

Characterization of the histone core complex

11 Zachau, H. G., G. Acs, and F. Lipmann, these PROCEEDINGS, 44, 885 (1958). 12 Zameenik, P. C., L. I. Hecht and M. L. Stephenson, Acta Union Internationale contre le Cancer, 16, 1121 (1960). 13 Hecht, L. I., M. L. Stephenson, and P. C. Zameenik, these PROCEEDINGS, 45, 505 (1959). 14 Smith, K. C., E. Cordes, and R. S. Schweet, Biochim. et Biophys. Acta, 33, 286 (1959). 11 Holley, R. W., and S. H. Mlerrill, J. Am. Chem. Soc., 81, 753 (1959). 16 Lipmann, F., W. C. Hfilsmann, G. Hartmann, H. G. Boman, and G. Acs, J. Cell. Comp. Physiol., 54, 75 (1959). 17 Cantoni, G. L., Nature, 188, 300 (1960). 18 Nishiyama, K., T. Okamoto, I. Watanabe, and M. Takanami, Biochim. et Biophys. Acta, 47, 193 (1961). 19 Hartmann, G., and U. Coy, Biochim. et Biophys. Acta, 47, 612 (1961). 20 Ofengand, E. J., M. Dieckmann, and P. Berg, J. Biol. Chem., 236, 1741 (1961). 21 Everett, G. A., S. H. Merrill, and R. W. Holley, Federation Proc., 20, 388 (1961). 22 Brown, G. L., A. V. W. Brown, and J. Gordon in Brookhaven Symposia in Biology, No. 12 (1959). 23 Monier, R., M. L. Stephenson, and P. C. Zameenik, Biochim. et Biophys. Acta, 43, 1 (1960). 24 Zameenik, P. C., M. L. Stephenson, and J. F. Scott, these PROCEEDINGS, 46, 811 (1960). 25 Saponara, A., and R. M. Bock, Federation Proc., 20, 356 (1961). 26 von Portatius, H., P. Doty, and M. L. Stephenson, J. Am. Chem. Soc., 83, 3351 (1961). 27 Porath, J., and P. Flodin, Nature, 183, 1657 (1959). 28 MCKernan, W. M., and C. R. Ricketts, Biochemt. J., 76, 117 (1960). 29 Porath, J., and E. B. Lindner, Nature, 191, 69 (1961). 30 Kirby, K. S., Biochem. J., 64, 405 (1956). 31Gierer, A., and G. Schramm, Nature, 177, 702 (1956). 32 Holley, R. W., J. Apgar, B. P. Doctor, J. Farrow, M. A. Marini, and S. H. Merrill, J. Biol. Chem., 236, 200 (1961). 33 Porath, J., Biochim. et Biophys. Acta, 39, 193 (1960). 34 Lowry, 0. H., N. J. Rosebrough, A. L. Farr, and R. J. Randall, J. Biol. Chem., 193, 265 (1951). 35 Scott, J. F., A. P. Fraccastoro, and E. B. Taft, J. Histochem. and Cytochem., 4, 1 (11956). 36 Hecht, L. I., P. C. Zameenik, M. L. Stephenson, and J. F. Scott, J. Biol. Chem., 233, 954 (1958). 37 Tissieres, A., J. Mol. Biol., 1, 365 (1959). 31 Dunn, D. B., J. D. Smith, and P. F. Spahr, J. Mol. Bicl., 2, 113 (1960). 39 Cox, R. A., and U. Z. Littauer, J. Mol. Biol., 2, 166 (1960). 40 Brown, G. L., and G. Zubay, J. Mol. Biol., 2, 287 (1960). 41 Yu, C-T., and P. C. Zameenik, Biochim. et Biophys. Acta, 45, 148 (1960).

https://www.pnas.org/content/pnas/47/10/1635.full.pdf

Paul Doty

Papers

Characterization of the histone core complex

THE OPTICAL ROTATORY DISPERSION OF RIGHT-HANDED α-HELICES IN SPERM WHALE MYOGLOBIN

Highly specific transcription of globin sequences in isolated reticulocyte nuclei

On the Nature of the Structural Element of Collagen

Studies on Synthetic Polypeptide Antigens: II. THE IMMUNOCHEMICAL PROPERTIES OF A GROUP OF LINEAR SYNTHETIC POLYPEPTIDES