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Biomedical subjects

A M Bobst

Publications and source records attributed to A M Bobst.

At least 37 records · Page 2Linked to original sources
PubMed1986

Redox-active daunomycin-spin-labeled nucleic acid complexes.

Interaction studies between daunomycin (DM) and enzymatically spin-labeled nucleic acid duplexes reveal two modes of binding by electron spin resonance (ESR) spectroscopy. At a low drug/nucleotide (D/N) ratio, the drug binds in the intercalative mode with only a slight reduction in base mobility. Saturation in the intercalative mode is achieved at a lower D/N ratio for B' DNA than for B DNA. After full intercalation, further addition of DM seems to destabilize the helix and to allow the formation of redox-active DM stacks complexed to the nucleic acid lattice. These stacks will irreversibly oxidize all the nitroxides covalently bound to the 4- or 5-position of the pyrimidine base. Interactions between DM and spin-labeled single-stranded nucleic acids lead directly to the formation of redox-active complexes, while mixing of the drug with spin-labeled nucleic acid building blocks not incorporated in a nucleic acid lattice causes no ESR signal change. Complete disappearance of the ESR signal of spin-labeled nucleic acids extrapolates to a D/N value which is a constant for a particular lattice system and is independent of spin-labeling content.

DNA↗
PubMed1986

Spin probes as mechanistic inhibitors and active site probes of thymidylate synthetase.

C-4- and C-5-substituted analogues of dUMP were examined as inhibitors of thymidylate synthetase and as topographical probes of its active site by electron spin resonance (ESR). The C-5-substituted spin-labeled analogues pDUAP (2) and a pDUTT (3) as well as the unlabeled AAdUMP (1) were competitive inhibitors with Ki's of 9.2, 89, and 7.9 microM, respectively. The C-4-spin-labeled pls4dU (4) displayed no inhibition activity. Scatchard plots as determined by ESR gave similar association constants for 2 (Kassoc = 1.9 X 10(5) M-1) and for 3 (Kassoc = 2.4 X 10(5) M-1). Both of these values are similar to the Kassoc of FdUMP indicating that the bulky substituent in position 5 does not interfere with the formation of the binary complex. The enzyme-C-5-spin-labeled nucleotide complexes indicate the presence of similarly immobilized spin labels by ESR, whereas no binding and immobilization were noticed with the C-4-spin-labeled nucleotide. A model for the active-site geometry of the enzyme was derived which suggests that the C-5 substituents point toward the opening of the binding cavity whose depth is at least 12 A. Also, the approximate 10-fold increased inhibitory activity of 2 as compared to that of 3 may be attributed to the significant electron withdrawing properties of the C-5 substituent in 2. Finally, the set of probes used for the binding and inhibition of thymidylate synthetase gives direct experimental evidence that an electron-withdrawing C-5 substituent primarily affects the formation of the ternary complex and will not substantially influence the stability of the binary complex.

Binding Sites↗
PubMed1985

Local base dynamics and local structural features in RNA and DNA duplexes.

Local base motion and local structural base information are derived with a simple motional model from site specifically spin-labeled polyribo- and polydeoxyribonucleotides. The model was developed earlier for some nucleic acids and has now been applied to analyze 22 different nucleic acid systems. We conclude that the base motion of the spin-labeled nucleotide in single-stranded RNA, DNA, or non-base-paired bases in duplexes is of the order of 1 ns and that its base mobility decreases by about a factor of 4 upon base pairing. Also, the tether motion of the probe is slower in an RNA than in a DNA duplex.

DNA↗
PubMed1985

Variability in the nucleic acid binding site size and the amount of single-stranded DNA-binding protein in Escherichia coli.

The Escherichia coli single-stranded DNA binding protein (SSB), essential for DNA replication, recombination and repair, can undergo a thermally induced irreversible conformational change which does not eliminate its biological activity, but changes the number of nucleotides it covers (binding site size) when binding to a single-stranded nucleic acid lattice. The binding site size of native and conformationally changed SSB was also found to be a function of the molecular mass of the polynucleotide, an observation which is unusual for single-stranded DNA binding proteins and will greatly affect the affinity relationship of this protein for nucleic acids. A radioimmunoassay used to quantitate in SSB level in cells revealed the number of SSB tetramers to be larger than initial estimates by a factor of as much as six. All these data suggest that the biological role of SSB and its mechanism of action is by far more complex than originally assumed.

Binding Sites↗
PubMed1985

Molecular dynamics in protein-single stranded DNA complexes. Two distinct nucleoside mobilities, in poly(deoxythymidylic acid)-poly-L-lysine complexes.

Stoichiometric amounts of poly-L-lysine were added to site-specifically spin labeled single stranded nucleic acids and the resulting complexes analyzed by electron spin resonance spectroscopy (ESR). The nucleic acids were spin labeled to different extents and with labels of varying tether length. The ESR data are used to determine nucleoside dynamics and some structural features in these complexes. It is concluded that two distinct base mobilities exist in the complexes; one set is characterized by a mean correlation time tau -R = 2 ns, and the other one by a tau -R greater than or equal to 50 ns. A model is proposed which suggests that a poly-L-lys single stranded nucleic acid complex consists of low mobility segments flanked by more mobile bases. An interesting feature of the proposed model is its applicability to explain ESR data of single strand binding protein-spin labeled nucleic acid complexes, which can also be interpreted in terms of two distinct nucleoside mobility states. It is hypothesized that this phenomenon could be of biological significance for the release of protein ligands from a protein-nucleic acid complex.

Binding Sites↗
PubMed1985

Molecular dynamics in protein-single stranded DNA complexes. Two distinct nucleoside mobilities in poly(deoxythymidylic acid)-gene 5 protein complexes.

A set of differently spin labeled (dT)n is used to evaluate thymidine dynamics and some of the structural features in a (dT)n-gene 5 protein complex. ESR evidence is presented that only one of the four thymidine residues bound in the DNA binding channel shows strong immobilization, whereas the other three display significant mobility of the order of nanoseconds. It is hypothesized that the accessability of such mobile bases could be critical to the recognition of the (dT)n-gene 5 protein complex in auxiliary interactions with other proteins and competitive DNAs.

Binding Sites↗
PubMed1984

Nucleic acid binding affinity of fd gene 5 protein in the cooperative binding mode.

A sensitive ESR method which allows a direct quantitative determination of nucleic acid binding affinities of proteins under physiologically relevant conditions has been applied to the gene 5 protein of bacteriophage fd. This was achieved with two spin-labeled nucleic acids, (ldT, dT)n and (lA,A)n, which served as macro-molecular spin probes in ESR competition experiments. With the two different macromolecular spin probes, it was possible to determine the relative apparent affinity constants, Kapp, over a large affinity domain. In 20 mM Tris X HCl (pH 8.1), 1 mM sodium EDTA, 0.1 mM dithiothreitol, 10% (w/v) glycerol, 0.05% Triton, and 125 mM NaCl, the following affinity relationship was observed: K(dT)napp = 10(3) KfdDNAapp = 2 X 10(4) K(A)napp = 6.6 X 10(4) KrRNAapp = 1.5 X 10(5) KR17RNAapp. Increasing the [NaCl] from 125 to 200 mM caused considerably less tight binding of gene 5 protein to (lA,A)n, and a typical cooperative binding isotherm was observed, whereas at the lower [NaCl] used for the competition experiments, the binding was essentially stoichiometric. A computer fit of the experimental titration data at 200 mM NaCl gave an intrinsic binding constant, Kint, of 1300 M-1 and a cooperativity factor, omega, of 60 (Kint omega = Kapp) for (lA,A)n.

Coliphages↗
PubMed1984

Dipsticking the major groove of DNA with enzymatically incorporated spin-labeled deoxyuridines by electron spin resonance spectroscopy.

Site-specifically spin-labeled deoxyuridine triphosphates with tethers of different lengths were synthesized and then enzymatically incorporated with terminal transferase to form a spin-labeled poly(dT) copolymer. The spin-labeled copolymers were annealed with poly(dA) to form a duplex, which was analyzed by electron spin resonance spectroscopy in a solution of low ionic strength. The spin labels are attached in position 5 of the deoxyuridine and protrude into the major groove. Based on the correlation between tether length of the spin label and the electron spin resonance lineshape, we show that the depth of the major groove of a DNA in its B-form is about 8 A in solution, which is in good agreement with X-ray fiber studies. We also conclude, based on electron spin resonance lineshape simulation data, that the correlation time of the bases in a DNA duplex is of the order of nanoseconds.

DNA↗
PubMed1984

Affinity of reverse transcriptase for some polynucleotide inhibitors.

The relative affinity of avian myeloblastosis virus reverse transcriptase for (U)n and a series of (U)n analogs has been measured directly in solution under conditions previously used to demonstrate the inhibitory properties of these polynucleotides. The affinities were measured by electron spin resonance through a quantitative competition approach where the concentration of each polynucleotide required to compete with the macromolecular spin probe (ls4U,U)n for reverse transcriptase was observed. Using this approach the following relative affinities were determined: K(dUfl)n = 1.6K(dUz)n = 13K(dT)n = 20K(U)320-640 = 57K(dU)n = 167K(U)80 greater than 167K(Um)n These results show that the affinity of (U)n for reverse transcriptase is affected by modifying the (U)n matrix and by the molecular weight of (U)n. In addition, the effect of some factors such as Mg+2 and salt on the polynucleotide affinity for the enzyme was measured. The results show that the same binding, i.e., the fraction of saturation F as a function of the nanomoles of reverse transcriptase added, was observed in the presence or absence of Mg+2, whereas increasing the KCl concentration from 0.04 to 0.5M completely dissociates the polynucleotide X enzyme complex.

Avian Myeloblastosis Virus↗
PubMed1983

Interaction of polymerases with 2'-deoxyuridine-5'-triphosphate spin-labeled at the 5-position.

2'-Deoxyuridine-5'-triphosphate spin-labeled at the 5-position with N-[1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl]-O- was found to be an inhibitor of some DNA and RNA polymerases including avian myeloblastosis virus reverse transcriptase. Furthermore, the spin-labeled nucleotide was found to be incorporated internally into polydeoxythymidylic acid via reverse transcriptase to an extent of 1.0 spin-labeled base per 10(3) bases. The incorporation, monitored by electron spin resonance, is analogous to some other nucleotide inhibitors of polymerases, and the results indicate that it may be feasible to obtain sequence specific, spin-labeled DNA, enzymatically.

Animals↗
PubMed1983

A low-cost microcomputer-based data acquisition and analysis system for an electron spin resonance spectrometer: data handling of dilute spin labeled nucleic acids.

This article describes the construction of an inexpensive and reliable data acquisition system for a Varian E-line Century Series ESR spectrometer utilizing an Apple II Plus microcomputer. All necessary hardware is readily available and used without modification. A BASIC program for routine collection, display, plotting and disk storage of experimental data has been written and subsequently compiled into machine code for high speed operation. The interface offers distinct advantages in spectral resolution as well as instrument control. An example of signal enhancement via computer controlled time averaging is presented for a spin labeled DNA experiment. The technique has recently been applied to studies of relative binding affinities of gene-32 protein for various spin-labeled polynucleotides.

Bacteriophage lambda↗
PubMed1982

Nucleic binding affinity of bacteriophage T4 gene 32 protein in the cooperative binding mode.

This study reports on various parameters which affect the binding stoichiometry for complexes of bacteriophage T4 gene 32 protein (P32) and single stranded polynucleotides (determined by UV absorbance and fluorescence quenching) and presents results of a quantitative electron spin resonance assay to determine physiologically effective binding affinity differences of nucleic acid binding proteins. The assay employs macromolecular spin probes (spin-labeled nucleic acids) which are used to determine the fraction of saturation in competition experiments with unlabeled nucleic acids. It was found that the fraction of complexed spin-labeled polynucleotides can be directly monitored by ESR with a two-component analysis approach when ligands such as poly(L-lysine), gene 5 protein (P5) of filamentous bacteriophage fd, and gene 32 protein (P32) of bacteriophage T4 are used. The ESR data unequivocally show that: 1) the binding stoichiometry for poly(L-lysine), P5 and P32 is nucleotide/lysine, 4 nucleotides/P5 monomer, and 10 nucleotides/P32 monomer, respectively; and 2) under physiologically relevant buffer conditions the relative affinity of P32 in the cooperative binding mode for polythymidylic acid is about 4 times greater than for polydeoxyinosinic acid and about 12 times greater than for polyinosinic acid, and the relative affinity of P32 for polydeoxyinosinic acid is about 3 times greater than for polyinosinic acid.

Electron Spin Resonance Spectroscopy↗
PubMed1981

Protein synthesis and competitive ESR binding studies with E. coli ribosomes and spin-labeled polynucleotides.

Enzymatically prepared spin labeled copolymers of (U)n were tested for their ability to direct polyphenylalanine synthesis in vitro using E. coli B enzymes and ribosomes. Spin labeling of the C5 position using (RUGT,U)n (1:100) or (RUTT,U)n (1:100) did not alter the amount of polyphenylalanine formed in comparison to (U)n. In contrast, the C4 spin labeled copolymer (ls4U,U)n (1:100) reduced phenylalanine incorporation by 70-75% of the (U)n control levels. ESR monitoring of competitive ribosome binding to equimolar mixtures of polynucleotides was demonstrated with the macromolecular probe (DUTT,dT)n (1:100), the DNA analogue of (RUTT,U)n. The ESR competition approach showed that the affinity of the ribosomes was essentially the same for (dT)n, (A,U,G)n, and (A,U,G)n + tRNArmet.

Bacterial Proteins↗
PubMed1981

Interferon induction by poly(inosinic acid).poly(cytidylic acid) segmented by spin-labels.

Poly(inosinic acid).poly(cytidylic acid) [(I)n.(C)n] duplexes of which the (C)n strand was modified to various degrees chemically or enzymatically with nitroxide radicals (spin-labels) were evaluated for interferon-inducing activity. Upon annealing of the chemically modified (C)n, (1C,Cx)n (X = 1000 or 16), with (I)n, the interferon-inducing activity was similar to that of (I)n.(C)n in PRK cell cultures. However, to overcome hydrolysis of the spin-label linkage in (1C,Cx)n, and enzymatic approach was taken to synthesize (1S(4)U,Cx)n copolymers with x = 100, 38, 16, and 8. The (1s(4)U,Cx)n copolymers were chemically stable, and upon annealing with (I)n the correlation time of the nitroxide moiety in (I)n. (1s(4)U,Cx)n was determined. A comparison of this correlation time with that measured for (RUGT,U100)n.(A)n, which contains the nitroxide moiety in position 5 of the U moiety, suggests that the 1s(4)U residue is in a nonintrahelical conformation and partitions the duplex into double-helical segments of varying size. The interferon-inducing activity of (I)n. (1s(4)U,Cx)n was evaluated in primary rabbit kidney, human skin fibroblast (strain VGS), and mouse L-929 cell cultures as well as in rabbits. The 1s(4)U residue did not cause a significant change in the interferon induction as compared to (I)n.(C)n in most systems tested unless x less than 16. These findings indicate that double-helical segments of approximately 16 base pairs partitioned by nonintrahelical 1s(4)U residues suffice to trigger the interferon response in all systems studied.

Animals↗