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 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.

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 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.

Interactions between DNA-bound trimers of the yeast heat shock factor

1994 ◽  
Vol 14 (1) ◽  
pp. 501-508
Author(s):  
J J Bonner ◽  
C Ballou ◽  
D L Fackenthal
Keyword(s):  
Heat Shock ◽  
Protein Complexes ◽  
Consensus Sequence ◽  
The Other ◽  
Inverted Repeats ◽  
Electrophoretic Mobilities ◽  
Naturally Occurring ◽  
Initial Identification ◽  
Dyad Symmetry ◽  
Chemical Cross Linking

The heat shock transcription factor (HSF) is a trimer that binds to DNA containing inverted repeats of the sequence nGAAn. HSF can bind DNA with the sequence nGAAnnTTCn or with the sequence nTTCnnGAAn, with little preference for either sequence over the other. However, (nGAAnnTTCn)2 is considerably less active as a heat shock response element (HSE) than is (nTTCnnGAAn)2. The electrophoretic mobilities of DNA-protein complexes and chemical cross-linking between protein monomers indicate that the sequence (nGAAnnTTCn)2 is capable of binding a single HSF trimer. In contrast, the sequence with higher biological activity, (nTTCnnGAAn)2, is capable of binding two trimers. Thus, the ability of four-nGAAn-element HSEs to bind one or two trimers depends on the permutation with which the elements are presented. A survey of naturally occurring HSEs shows the sequence (nTTCnnGAAn)2 to be the more prevalent. We suggest that the greater ability of one permutation over the other to bind two HSF trimers accounts for the initial identification of the naturally occurring heat shock consensus sequence as a region of dyad symmetry.

scholarly journals The Glucosamine Controversy; A Pharmacokinetic Issue

2011 ◽  
Vol 14 (2) ◽  
pp. 264 ◽  
Author(s):  
Ali Aghazadeh-Habashi ◽  
Fakhreddin Jamali
Keyword(s):  
Clinical Trial ◽  
Animal Studies ◽  
The Other ◽  
Naturally Occurring ◽  
Assessment Metrics ◽  
Disease Modifying ◽  
Clinical Trial Results ◽  
Higher Doses ◽  
Positive Results ◽  
Rule Out

Glucosamine (GlcN) is a naturally occurring aminosugar that is widely used to treat osteoarthritis despite controversial clinical trial results. Animal studies, on the other hand, unequivocally suggest anti-inflammatory and disease modifying effects for GlcN. Many explanations have been offered as to the root of the controversy. They include superiority of a crystalline sulphate salt over HCl, industry bias, insensitive assessment metrics and poor methodology. Herein, we rule out a difference in bioequivalence between GlcN salts and that of chemically equivalent doses and suggest additional factors; i.e., inconsistency in the chemical potency of some products used, under-dosing of patients as well as variable and erratic bioavailability indices for the lack of GlcN efficacy observed in some studies. Clinical trials using higher doses of pharmaceutical grade GlcN or formulations with greater bioavailability should yield positive results. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.

scholarly journals Municipal Representatives’ Accounts of Decision-Making Practices during Geriatric Case Conferences

2017 ◽  
Vol 23 (45) ◽  
pp. 129
Author(s):  
Søren Beck Nielsen
Keyword(s):  
Senior Citizens ◽  
General Characteristic ◽  
The Other ◽  
Residential Home ◽  
Residential Homes ◽  
Social Actors ◽  
Naturally Occurring ◽  
Case Conferences ◽  
The Relationship ◽  
Elderly Citizen

This article addresses questions of elucidation in talk-in-interaction. How do social actors give accounts of what they are doing? To what degree do actors sustain a taken-for-granted level of reasoning? The analysis is based upon naturally occurring data consisting of a corpus of audio recorded case conferences at various geriatric wards in Danish hospitals. The article elaborates one of the important insights of Harold Garfinkel regarding the relationship between discourse and social interaction: as a general characteristic, people tend to treat their fellow interlocutors’ conversational contributions as adequate for-all-practical-purposes. Specifically, the article investigates how Danish municipal representatives account for their decisions about whether or not senior citizens are to be referred to residential homes. This practice, I demonstrate, is characterized by non-explicitness with regards to rules and regulations. Instead, municipal representatives make use of developmental discourse: a worsened condition is used to justify a referral to a residential home. On the other hand, an improved condition is used to justify that an elderly citizen is not referred to a residential home.

scholarly journals Medical treatment of gallstones

1978 ◽  
Vol 16 (18) ◽  
pp. 69-71
Keyword(s):  
Medical Treatment ◽  
Bile Acids ◽  
Cholic Acid ◽  
Chenodeoxycholic Acid ◽  
The Other ◽  
Naturally Occurring ◽  
Made In

Chenodeoxycholic acid (CDCA) (Chendol - Weddel) is one of two naturally occurring ‘primary’ bile acids (the other being cholic acid) made in the liver from cholesterol. CDCA is synthesised commercially from cholic acid and prescribed as gelatin-coated capsules containing 125 mg CDCA.

Coordinated righting behaviour in locusts

2001 ◽  
Vol 204 (4) ◽  
pp. 637-648 ◽  
Author(s):  
A.A. Faisal ◽  
T. Matheson
Keyword(s):  
Driving Force ◽  
Flat Surface ◽  
Longitudinal Axis ◽  
Upright Position ◽  
The Body ◽  
The Other ◽  
Legged Robots ◽  
Naturally Occurring ◽  
Key Features ◽  
Low Levels

A locust placed upside down on a flat surface uses a predictable sequence of leg movements to right itself. To analyse this behaviour, we made use of a naturally occurring state of quiescence (thanatosis) to position locusts in a standardised upside-down position from which they spontaneously right themselves. Locusts grasped around the pronotum enter a state of thanatosis during which the limbs can be manipulated into particular postures, where they remain, and the animal can be placed upside down on the ground. When released, thanatosis lasts 4–456 s (mean 73 s) before the animal suddenly becomes active again and rights itself within a further 600 ms. Thanatosis is characterised by very low levels of leg motor activity. During righting, one hind leg provides most of the downward force against the ground that rolls the body around a longitudinal axis towards the other side. The driving force is produced by femoral levation (relative to the body) at the trochanter and by tibial extension. As the animal rolls over, the hind leg on the other side is also levated at the trochanter, so that it does not obstruct the movement. The forelegs and middle legs are not required for successful righting but they can help initially to tip the locust to one side, and at the end of the movement they help stop the roll as the animal turns upright. Individual locusts have a preferred righting direction but can, nevertheless, roll to either side. Locusts falling upside down through the air use both passive and active mechanisms to right themselves before they land. Without active movements, falling locusts tend to rotate into an upright position, but most locusts extend their hind leg tibiae and/or spread their wings, which increases the success of mid-air righting from 28 to 49 % when falling from 30 cm. The rapid and reliable righting behaviour of locusts reduces the time spent in a vulnerable upside-down position. Their narrow body geometry, large hind legs, which can generate substantial dorsally directed force, and the particular patterns of coordinated movements of the legs on both sides of the body are the key features that permit locusts to right themselves effectively. The reliability of autonomous multi-legged robots may be enhanced by incorporating these features into their design.

scholarly journals Testing of microbial additives in the rooting of Norway spruce (Picea abies [L.] Karst.) stem cuttings

2011 ◽  
Vol 57 (No. 12) ◽  
pp. 555-564 ◽  
Author(s):  
I. Repáč ◽  
J. Vencurik ◽  
M. Balanda
Keyword(s):  
Norway Spruce ◽  
Shoot Growth ◽  
Growth Parameters ◽  
Alginate Bead ◽  
Block Design ◽  
The Other ◽  
Stem Cuttings ◽  
Naturally Occurring ◽  
Randomized Complete Block Design ◽  
Ecm Fungi

&nbsp;Laboratory-produced alginate-bead inoculum of ectomycorrhizal (ECM) fungi Cortinarius sp. and&nbsp;Gomphidius glutinosus, fungal commercial products ECtovit<sup>&reg; </sup>and Trichomil<sup>&reg;</sup>, bacterial commercial product BactoFil&nbsp;B<sup>&reg;</sup>, and commercial rooting stimulator Vetozen<sup>&reg;</sup> were applied to a peat-perlite (1:2, v:v) rooting substrate of Norway spruce stem cuttings collected from 4-year-old nursery-grown seedlings immediately before the insertion of cuttings into the substrate. The application of beads free of fungi and the substrate without an additive were the other treatments. The cuttings were rooted in vessels (60 cuttings per vessel, 180 per treatment) placed in a glasshouse and arranged in a randomized complete block design. The cuttings were estimated for one growing season (approximately for 26 weeks) after their insertion into the rooting substrate. Rooting % of the cuttings ranged from 45 (mycelium-free beads) to 75 (control) according to treatments, 64 on average. No significant differences among treatments were found in % of ECM morphotypes, total ECM colonization of roots (%), and growth parameters of shoots and roots of the cuttings. The applied microbial additives were not sufficiently efficient to form treatment-related ectomycorrhizas that were formed by naturally occurring ECM fungi. Inoculation by the ECM fungus Cortinarius sp. and application of Trichomil had a partial stimulative effect on the shoot growth of cuttings. Shoot and root growth parameters were not significantly correlated with total ECM colonization, except for a negative dependence of the root number in Trichomil treatment. A higher concentration of K but lower concentrations of Ca and Mg in Ectovit treatment than in the other treatments were detected.&nbsp; &nbsp;

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.

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