The topological trapping of circular DNAs on agarose: Unexpected restrictions on DNA rotation

1978 ◽  
Vol 56 (6) ◽  
pp. 585-591 ◽  
Author(s):  
Jeremy S. Lee ◽  
A. Richard Morgan
Keyword(s):  
Secondary Structure ◽  
Binding Constant ◽  
Binding Assay ◽  
Sodium Perchlorate ◽  
Binding Constants ◽  
The Other ◽  
Calf Thymus ◽  
Potential Applications ◽  
Open Circular ◽  
Circular Dnas

DNA linked to an insoluble matrix has many potential applications. In some cases, it is highly desirable that the DNA be chemically unaltered, and for this reason, we have developed methods for topologically trapping circular DNAs on agarose. Open circular (oc) DNA containing at least one nick is readily trapped on agarose which has been heated or dissolved in sodium perchlorate to destroy secondary structure and then gelled by cooling or dialysis respectively. On the other hand, covalently closed circular (ccc) DNA of superhelix density −0.12 (PM2 DNA) is only poorly trapped unless first relaxed by topoisomerases or with the appropriate addition of an intercalating drug. When the oc DNA – agarose was used in a procedure for rapidly obtaining binding constants of drugs to DNA, the binding constant of ethidium was found to be considerably less than that expected. On addition of calf thymus topoisomerase to the binding-assay mixture, the ethidium-binding constant increased to the expected value. Thus, although free oc DNA is topologically unrestricted, oc DNA trapped in agarose must be rotationally constrained such that addition of ethidium introduced supercoils. The nature of these constraints is discussed with respect to the known structure of agarose bihelices.

scholarly journals Interaction between synthetic analogues of quinoxaline antibiotics and nucleic acids. Changes in mechanism and specificity related to structural alterations

1978 ◽  
Vol 173 (1) ◽  
pp. 129-144 ◽  
Author(s):  
J S Lee ◽  
M J Waring
Keyword(s):  
Binding Constant ◽  
Dimethyl Ester ◽  
Sedimentation Coefficient ◽  
Binding Constants ◽  
The Other ◽  
Sequence Specificity ◽  
Synthetic Dna ◽  
Cross Bridge ◽  
Naturally Occurring ◽  
Triostin A

The interaction with DNA of six chemically synthesized derivatives of the quinoxaline antibiotics was investigated. Five of the compounds bound only weakly to DNA or not at all; for these substances spectrophotometric measurements, sedimentation studies with closed circular duplex bacteriophage-PM2 DNA and thermal-denaturation profiles were used to determine limits fot the binding constants. No interaction could be detected with two products of degradation of echinomycin (quinomycin A), one of which, echinomycinic acid dimethyl ester, had the lactone linkages opened, whereas the other retained an intact octapeptide ring but had a broken cross-bridge. The other compounds studied were des-N-tetramethyl-triostin A (‘TANDEM’) and its derivatives. A derivative of ‘TANDEM’ IN WHICH benzyloxycarbonyl moieties replace both quinoxaline chromophores had binding constants to nucelic acids in the range 10(2)–10(3)-1, whereas no interaction could be detected for a benzyloxycarbonyl derivative that, in addition, had the cross-bridge broken. The derivative of ‘TANDEM’ with L-serine in place of D-serine in both positions showed no detectable interaction with Clostridium perfringens DNA, whereas the binding constant to poly(dA-dT) was approx 2 × 10(3)M-1. ‘TANDEM’ itself bound strongly to DNA, and the bathochromic and hypochromic shifts in its u.v.-absorption spectrum in the presence of DNA were similar to those seen with echinomycin. From the effect on the sedimentation coefficient of closed circular duplex bacteriophage-PM2 DNA the mechanism of binding was shown to involve bifunctional intercalation, typical of the naturally occurring quinoxaline antibiotics. Solvent-partition analysis was used to determine binding constants for the interaction between ‘TANDEM’ and a variety of natural and synthetic DNA species. The pattern of specificity thus revealed differed markedly from that previously found with the naturally occurring quinoxaline antibiotics. Most striking was the evident large preference for (A + T)-rich DNA species, in complete contrast with echinomycin and triostin A. The highest binding constant was found for poly(dA-dT), the interaction with which appeared highly co-operative in character. The conformations adopted by those quinoxaline compounds that bind strongly to DNA were examined withe aid of molecular models on the basis of results derived from n.m.r. and computer studies. It appears that the observed patterns of base-sequence specificity are determined, at least in part, by the structure and conformation of the sulphur-containing cross-bridge.

scholarly journals Responses of the Pheromone-Binding Protein of the Silk Moth Bombyx mori on a Graphene Biosensor Match Binding Constants in Solution

Sensors ◽  
2021 ◽  
Vol 21 (2) ◽  
pp. 499
Author(s):  
Caroline Bonazza ◽  
Jiao Zhu ◽  
Roger Hasler ◽  
Rosa Mastrogiacomo ◽  
Paolo Pelosi ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Binding Protein ◽  
Binding Constants ◽  
Isoamyl Acetate ◽  
The Other ◽  
Oxide Surface ◽  
Binding Assays ◽  
Pheromone Binding Protein ◽  
Silk Moth ◽  
Good Agreement

An electronic biosensor for odors was assembled by immobilizing the silk moth Bombyx mori pheromone binding protein (BmorPBP1) on a reduced graphene oxide surface of a field-effect transistor. At physiological pH, the sensor detects the B. mori pheromones, bombykol and bombykal, with good affinity and specificity. Among the other odorants tested, only eugenol elicited a strong signal, while terpenoids and other odorants (linalool, geraniol, isoamyl acetate, and 2-isobutyl-3-methoxypyrazine) produced only very weak responses. Parallel binding assays were performed with the same protein and the same ligands, using the common fluorescence approach adopted for similar proteins. The results are in good agreement with the sensor’s responses: bombykol and bombykal, together with eugenol, proved to be strong ligands, while the other compounds showed only poor affinity. When tested at pH 4, the protein failed to bind bombykol both in solution and when immobilized on the sensor. This result further indicates that the BmorPBP1 retains its full activity when immobilized on a surface, including the conformational change observed in acidic conditions. The good agreement between fluorescence assays and sensor responses suggests that ligand-binding assays in solution can be used to screen mutants of a binding protein when selecting the best form to be immobilized on a biosensor.

New uses for brick-making clay materials from the Bailén area (southern Spain)

Clay Minerals ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 453-465 ◽  
Author(s):  
I. Gonzalez ◽  
E. Galan ◽  
A. Miras ◽  
P. Aparicio
Keyword(s):  
Particle Size ◽  
Iron Oxides ◽  
Raw Materials ◽  
The Other ◽  
Southern Spain ◽  
Other Hand ◽  
Floor Tiles ◽  
Potential Applications ◽  
Clay Materials

AbstractAn attempt has been made to assess new potential applications for the Bailén clays, traditionally used for manufacturing bricks, based on mineralogical, chemical, particle size, plasticity and firing results. Raw materials and mixtures used by the local factory were selected and tested with the addition of some diatomite, feldspar or kaolin. Based on their properties, clay materials from Bailén might be suitable for making porous red wall tiles, clinker, vitrified red floor tiles and porous light-coloured wall tiles by pressing; the first could be manufactured from the raw materials and mixtures currently used by the local manufactures. On the other hand, stoneware shaped by extrusion, such as perforated bricks, facing bricks and roofing tiles, can be also manufactured from the mixtures used at the factory if they contain 20-25% carbonate and small amounts of iron oxides; lightweight bricks require black and yellow clays with diatomite.

scholarly journals A Review of Bacteriochlorophyllides: Chemical Structures and Applications

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1293
Author(s):  
Chih-Hui Yang ◽  
Keng-Shiang Huang ◽  
Yi-Ting Wang ◽  
Jei-Fu Shaw
Keyword(s):  
Solar Cell ◽  
Energy Harvesting ◽  
Chemical Structure ◽  
The Other ◽  
Dye Sensitized Solar Cell ◽  
Synthetic Route ◽  
Chemical Structures ◽  
Dye Sensitized ◽  
Heme Synthesis ◽  
Potential Applications

Generally, bacteriochlorophyllides were responsible for the photosynthesis in bacteria. Seven types of bacteriochlorophyllides have been disclosed. Bacteriochlorophyllides a/b/g could be synthesized from divinyl chlorophyllide a. The other bacteriochlorophyllides c/d/e/f could be synthesized from chlorophyllide a. The chemical structure and synthetic route of bacteriochlorophyllides were summarized in this review. Furthermore, the potential applications of bacteriochlorophyllides in photosensitizers, immunosensors, influence on bacteriochlorophyll aggregation, dye-sensitized solar cell, heme synthesis and for light energy harvesting simulation were discussed.

Filarial DNA and its interaction with polyamines and antifilarial drugs

1997 ◽  
Vol 71 (4) ◽  
pp. 325-332 ◽  
Author(s):  
U. Pandya ◽  
J.K. Saxena ◽  
O.P. Shukla
Keyword(s):  
Escherichia Coli ◽  
Secondary Structure ◽  
Melting Temperature ◽  
Base Composition ◽  
Micrococcus Luteus ◽  
Gc Content ◽  
Setaria Cervi ◽  
Calf Thymus ◽  
Absorption Studies ◽  
Z Dna

AbstractThe interaction of DNA from filarial parasite Setaria cervi with polyamines was monitored by melting temperature (Tm) profile, condensation and B to Z DNA transition and compared with DNA of Escherichia coli, Micrococcus luteus and calf thymus having different GC content. Polyamines, viz. spermine and spermidine, stabilized the secondary structure of all DNAs as indicated by increase in Tm value. UV absorption studies indicated B to Z DNA transition in the presence of polyamines. The amount of polyamines required for B to Z transition was dependent upon base composition of DNA and charge of the polyamine. Filarial DNA (AT rich) required six times higher concentration of spermine as compared to GC rich DNA for B to Z DNA transition. Spermidine was not effective in causing transition of S. cervi DNA even at Spd:DNA-P ratio of 20. The antifilarial compound suramin significantly decreased melting temperature of filarial DNA as compared to GC rich DNAs of other parasites. Suramin adversely affected condensation and B to Z DNA transition of various DNAs but prior addition of polyamines protected the DNAs from the destabilizing effect of suramin.

scholarly journals Bifunctional intercalation and sequence specificity in the binding of quinomycin and triostin antibiotics to deoxyribonucleic acid

1978 ◽  
Vol 173 (1) ◽  
pp. 115-128 ◽  
Author(s):  
J S Lee ◽  
M J Waring
Keyword(s):  
Binding Constant ◽  
Binding Constants ◽  
Sequence Specificity ◽  
Peptide Antibiotics ◽  
Naturally Occurring ◽  
Binding Isotherms ◽  
Triostin A ◽  
Specificity Pattern ◽  
Intercalating Agents ◽  
Binding Curves

Quinomycin C, triostin A and triostin C are peptide antibiotics of the quinoxaline family, of which echinomycin (quinomycin A) is also a member. They all remove and reverse the supercoiling of closed circular duplex DNA from bacteriophage PM2 in the fashion characteristic of intercalating drugs, and the unwinding angle at I 0.01 is, in all cases, almost twice that of ethidium. Thus, as with echinomycin, they can be characterized as bifunctional intercalating agents. For the triostins this conclusion has been confirmed by measurements of changes in the viscosity of sonicated rod-like DNA fragments; the helix extension was found to be almost double that expected for a simple monofunctional intercalation process. For triostin A, further evidence for bifunctionality was derived from the cross-over point of binding isotherms to nicked circular and closed circular bacteriophage-PM2DNA. Binding curves for the interaction of quinomycin C and triostin A with a variety of synthetic and naturally occurring nucleic acids were determined by solvent-partition analysis, but triostin C was too insoluble in aqueous solution to make this method applicable. For quinomycin C the highest binding constant was found with Micrococcus lysodeikticus DNA, and its pattern of specificity among natural DNA species was broadly similar to that of echinomycin, although the binding constants were 2–6 times as large. For triostin A the highest binding constant was again found for M. lysodeikticus DNA, but the specificity pattern was quite different from that of the quinomycins. In particular, triostin A bound better to poly(dA-dT) than to the poly(dG-dC) whereas this order was reversed for quinomycin C. There was also evidence that the binding to poly(dA-dT) might be co-operative in nature. No significant interaction could be detected with poly(dA).poly(dT) or with RNA from Escherichia coli. Poly(dG).poly(dC) gave variable results, depending on the source of the polymer. The different patterns of specificity displayed by the quinomycins and triostins are tentatively ascribed to differences in their conformations in solution.

Host-guest interactions of cyclodextrins and metalloporphyrins: supramolecular building blocks toward artificial heme proteins

2004 ◽  
Vol 08 (02) ◽  
pp. 125-140 ◽  
Author(s):  
Huchen Zhou ◽  
John T. Groves
Keyword(s):  
Binding Constant ◽  
Molecular Design ◽  
Covalent Binding ◽  
Binding Constants ◽  
Building Blocks ◽  
Binding Pocket ◽  
Axial Ligand ◽  
Pyridyl Nitrogen ◽  
H Nmr ◽  
Self Assembled

Cyclodextrins are versatile building blocks for a variety of macromolecules due to the inclusion complexes that are formed with hydrophobic organic molecules. Cyclodextrin-porphyrin interactions are of particular interest since cyclodextrins can serve as a non-covalent binding pocket while metalloporphyrins could serve as the heme analogs in the construction of heme protein model compounds. Various approaches to the design and assembly of biomimetic porphyrin constructs are compared and contrasted in this minireview with a particular emphasis on self-assembled and porphyrin-cyclodextrin systems. Several recent advances from our laboratories are described in this context. A sensitive fluorescent binding probe, 6A-N-dansyl-permethylated-β-cyclodextrin (Dan-NH-TMCD), was found to form 2:1 complexes with the meso-tetraphenylporphyrins Mn(III)TCPP , Mn(III)TPPS and Mn(III)TF 4 TMAP with high binding constants. A perPEGylated cyclodextrin, heptakis(2,3,6-tri-O-2-(2-(2-methoxyethoxy)ethoxy)ethyl)-β-cyclodextrin (TPCD), has been shown by 1 H NMR spectroscopy to form a 1:1 complex with H 2 TCPP with a binding constant above 108M-1. Such a strong binding constant is the largest found for a 1:1 complex between a monomeric cyclodextrin and a guest. TPCD was also found to bind Mn(III)TCPP with a binding constant of 1.2 × 106 M -1. A novel, self-assembled hemoprotein model, hemodextrin is also described. The molecular design is based on a PEGylated cyclodextrin scaffold that bears both a heme-binding pocket and an axial ligand that binds an iron porphyrin. The binding constant for Fe (III) TPPS (iron(III) meso-tetra(4-sulfonatophenyl)porphyrin) by py-PPCD was determined to be 2 × 106 M -1. The pyridyl nitrogen of py-PPCD was shown to ligate to the iron center by observing signal changes in the Fe(II) -porphyrin 1 H NMR spectrum. This hemodextrin ensemble, a minimalist myoglobin, was shown to bind dioxygen reversibly and to form a stable ferryl species.

Computerized Fieldwork Data Base: Applications and Implications

1987 ◽  
Vol 54 (5) ◽  
pp. 263-267 ◽  
Author(s):  
Helen Polatajko ◽  
Marilyn Ernest ◽  
Joyce MacKinnon
Keyword(s):  
Data Base ◽  
Educational Programs ◽  
The Other ◽  
Other Hand ◽  
Resultant Data ◽  
Potential Applications ◽  
The One ◽  
The University ◽  
Professional Judgement

Fieldwork placement is a complicated and involved task. On the one hand, it requires insightful, professional judgement, but on the other hand, it includes numerous routine administrative and clerical tasks. To deal with fieldwork placement more efficiently and effectively it was decided to computerize the fieldwork placement system at the University of Western Ontario, London, Ontario. This paper describes the system developed and the resultant data base. The potential applications of the data base and the implications for students, facilities, educational programs, professional governing bodies and research are discussed.

scholarly journals The Radiative, Cloud, and Thermodynamic Properties of the Major Tropical Western Pacific Cloud Regimes

2005 ◽  
Vol 18 (8) ◽  
pp. 1203-1215 ◽  
Author(s):  
Christian Jakob ◽  
George Tselioudis ◽  
Timothy Hume
Keyword(s):  
Thermodynamic Properties ◽  
Thermodynamic Characteristics ◽  
The Other ◽  
Western Pacific ◽  
Cloud Properties ◽  
Tropical Western Pacific ◽  
Potential Applications ◽  
Shallow Clouds ◽  
Atmospheric Radiation Measurement ◽  
Cloud Regimes

Abstract This study investigates the radiative, cloud, and thermodynamic characteristics of the atmosphere separated into objectively defined cloud regimes in the tropical western Pacific (TWP). A cluster analysis is applied to 2 yr of daytime-only data from the International Satellite Cloud Climatology Project (ISCCP) to identify four major cloud regimes in the TWP region. A variety of data collected at the Department of Energy’s Atmospheric Radiation Measurement Program (ARM) site on Manus Island is then used to identify the main characteristics of the regimes. Those include surface and top-of-the-atmosphere radiative fluxes and cloud properties derived from a suite of ground-based active remote sensors, as well as the temperature and water vapor distribution measured from radiosondes. The major cloud regimes identified in the TWP area are two suppressed regimes—one dominated by the occurrence of mostly shallow clouds, the other by thin cirrus—as well as two convectively active regimes—one exhibiting a large coverage of optically thin cirrus clouds, the other characterized by a large coverage with optically thick clouds. All four of these TWP cloud regimes are shown to exist with varying frequency of occurrence at the ARM site at Manus. It is further shown that the detailed data available at that site can be used to characterize the radiative, cloud, and thermodynamic properties of each of the regimes, demonstrating the potential of the regime separation to facilitate the extrapolation of observations at one location to larger scales. A variety of other potential applications of the regime separation are discussed.

scholarly journals Numerical Approach to the Kinematic Analysis of Deployable Structures Forming a Closed Loop

2006 ◽  
Vol 220 (7) ◽  
pp. 1045-1056 ◽  
Author(s):  
W W Gan ◽  
S Pellegrino
Keyword(s):  
Systematic Study ◽  
Numerical Scheme ◽  
Closed Loop ◽  
Numerical Approach ◽  
The Other ◽  
Deployable Structures ◽  
Potential Applications ◽  
Motion Range ◽  
Polygonal Shape ◽  
Spatial Linkages

This article is concerned with spatial linkages forming a closed loop. In one extreme configuration (deployed), these linkages form a frame of polygonal shape, such as a square or a hexagon, and in the other extreme (folded), configuration form a tight bundle. Throughout their motion range, they have mobility one. These linkages have potential applications for next-generation deployable spacecraft structures. The article presents a systematic study of the kinematics of closed-loop structures with these special properties and a numerical scheme for simulating their deployment without making any assumptions about particular symmetry features. The proposed simulation technique is applied to three examples that show different behaviour during deployment.

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