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R Römer

Publications and source records attributed to R Römer.

At least 19 recordsLinked to original sources
PubMed1985

NMR study of the drug-base overlap geometry in the dark complex of 8-methoxypsoralen and d(pApT)4.

The dark binding of 8-methoxypsoralen (MOP) to d(pApT)4 was investigated by 270-MHz 1H nuclear magnetic resonance (NMR) spectra. The continuous high-field shifts of the MOP resonances by d(pApT)4 at low temperatures indicate fast exchange between free and bound drug. The limiting complexation shifts of the various MOP protons between 0.36 (CH3) and 1.20 ppm (H5) are in the range expected for an intercalation complex. The NMR line widths of the MOP ring protons vary with the square of the observed complexation shifts (maximum at H5), indicating a dominant effect of the fast exchange between free and bound drug. The corresponding kinetic parameters agree with the values previously reported for a variety of other intercalators. The observed exchange broadenings were also used as a criterion to limit the uncertainty connected with fast averaging of the signals of the drug in potential multiple binding modes: A qualitatively different pattern of broadenings (minimum at H5) is expected from fast exchange between the two binding modes related by the short 2-fold quasi-symmetry axis of MOP. The measured complexation shifts were compared to theoretical values calculated on the basis of coplanar intercalation with base pair arrangements derived from typical published intercalation site geometries. The standard deviation between observed and calculated shifts was considerably smaller for asymmetrical intercalation between the bases of the same strand (less than or equal to 0.11 ppm) than for symmetrical intercalation between the base pairs (greater than or equal to 0.28 ppm).(ABSTRACT TRUNCATED AT 250 WORDS)

Darkness↗
PubMed1984

Escherichia coli single-stranded DNA binding protein is mobile on DNA: 1H NMR study of its interaction with oligo- and polynucleotides.

The interaction of the Escherichia coli single-stranded DNA binding protein (SSB) with oligo- and poly-nucleotides has been studied by 270-MHz 1H NMR spectroscopy and fast kinetic techniques. d(pT)8 and poly(dT) were used to study noncooperative and cooperative binding, respectively. The H6, H1', and CH3 resonances of d(pT)8 are high-field shifted by less than 0.05 ppm, and H8 and H2 of poly(dA) are low-field shifted upon complexation. The protein resonances remain virtually unshifted. The small shifts upon complexation provide no evidence for extensive stacking interactions between the nucleotide bases and aromatic amino acid side chains of SSB. The d(pT)8 and poly(dA) signals are broadened to about 30 Hz whereas the resonances of poly(dT) are broadened beyond detection upon stoichiometric complexation. Continuous broadening of all poly(dT) signals even at a 10-fold excess of poly(dT) indicates fast exchange of SSB between different binding sites. Dissociation and reassociation rates determined from stopped-flow experiments are too slow by at least 2 orders of magnitude to account for the experimental line widths. Therefore, we conclude that SSB translocates without dissociation from the DNA template. A model for the translocation is outlined. It is based on partial dissociation of octamer sections of poly(dT) from the complex with a rate constant as previously published for the dissociation of d(pT)8 from SSB.

DNA-Binding Proteins↗
PubMed1984

[Persistent infarct signs--obligate symptoms of heart wall aneurysm?].

Out of 19 cases the ECG of which on an average during 6.1 years demonstrated persisting signs of an infarction at stage I in 13 cases a comparison between clinical and ECG findings X-ray kymography and scintigraphy of the ventricle was possible. In 7 cases a congruence of the results was found. With regard to the differing findings on account of the clinical treatment, the ECG and the ejection fraction the greater diagnostic valency must be ascribed to the Tc-scintigraphy.

Adult↗
PubMed1977

Hydrogen-bonded protons in the tertiary structure of yeast tRNAPhe in solution.

Temperature-dependent lowfield proton magnetic resonance spectra of yeast tRNAPhe were recorded between 10 and 15 parts per million. Seven resonances of hydrogen-bonded protons disappeared reversibly under two sets of conditions where the selective broadening of tertiary structure resonances were predicted by temperature jump experiments. The seven resonances were assigned to the seven tertiary hydrogen bonds expected between 10 and 15 parts per million from the crystal structure of yeast tRNAPhe. Some of the non-Watson-Crick base pairs have unusual unshifted standard chemical shifts after the ring current contributions calculated from the crystal coordinates were subtracted. The differences of the chemical shifts of homologous tertiary structure base pairs in Escherichia coli tRNAfMet and yeast tRNAPhe give experimental evidence for details of the conformational differences postulated by model building on the basis of the x-ray coordinates of yeast tRNAPhe and sequence homologies.

Hydrogen Bonding↗
PubMed1975

Tertiary structure of tRNAPhe (yeast): kinetics and electrostatic repulsion.

Conditions were established that allowed the observation of the unfolding of the tertiary structure of tRNAPhe (yeast) without the interference of either secondary structure or low salt aberrant structures. Relaxation kinetics of tertiary structure melting show that the reaction proceeds according to co-operative all-or-none mechanism. The negative activation enthalpy of formation (delta H+ + R = -14 +/- 5 kcal/mol, -59 +/- 21 kJ/mol) implies a fast pre-equilibrium preceding the rate-limiting step. The ionic strength dependence of the corresponding rate constant demonstrates that most of the electrostatic repulsion characteristic of tertiary structure folding is overcome before the rate-limiting step is reached. On the other hand, most of the stabilizing enthalpy change occurs after the rate-limiting step. At the usual ionic strength (0.1 M Na+) tertiary structure folding is about 100 times slower than double-helix formation. Extrapolation of the rate constants to high ionic strengths, however, indicates that the dynamic differences between secondary and tertiary structure are only due to electrostatic repulsion. The stabilization of tertiary structure by alkaline salts is increased by decreasing the cationic radius. Double helices show virtually no dependence on the radius of monovalent cations. This indicates considerable geometric restrictions for the stabilization of tertiary structure.

Kinetics↗
PubMed1975

tRNA conformation and magnesium binding. A study of a yeast phenylalanine-specific tRNA by a fluorescent indicator and differential melting curves.

The binding of Mg2+ to tRNAPhe (yeast) in three conformational states was studied at 10, 30, 45, and 70 degrees C by the fluorescence indicator 8-hydroxyquinoline 5-sulphonic acid in the presence of 0.032 M monovalent cations (Na+). At temperatures below those characteristic for early melting (completely folded tRNA) the Scatchard plots are biphasic. They were well fitted by two classes of noninteracting binding sites with stability constants independent of temperature (KA = 9X10(4), KB = 6X10(3) M-1). In partially unfolded tRNA the strong binding process is co-operative. A single class of weak sites was found in the statistically coiled conformation at 70 degrees C (KB = 3.3X103 M-1). The total number of binding sites is 23 +/- 5; differences for the folded and unfolded conformations are smaller than 1. The influence of Mg2+ on the stability of the conformational elements of tRNAPhe (yeast) and its CCA-half (i.e. nucleotides 38--76) was determined by differential ultraviolet absorbance and depolarisation melting curves using the fluorescence of the Y base. Tertiary structure corresponding to early melting is stabilized by strongly bound Mg2+, whereas all other melting transitions are only influenced by Mg2+ bound at weak sites. The stability constants of tertiary structure obtained from the melting experiments can quantitatively be described by assuming that 5 +/- 1 non-interacting strong sites as characterized by the fluorescence titrations are converted to weak sites upon unfolding of the tertiary structure. Co-operative interaction of Mg2+ with the 5 strong sites in the folded conformation of tRNA can be ruled out. Strong binding of Mg2+ to completely folded tRNA does not produce a conformational transition changing ultraviolet absorbance, circular dichroism and sedimentation coefficient.

Binding Sites↗
PubMed1975

Kinetics of conformational changes in tRNA Phe (yeast) as studied by the fluorescence of the Y-base and of formycin substituted for the 3'-terminal adenine.

The kinetics of the melting transitions of tRNA Phe (yeast) were followed by the fluorescence of the Y-base and of formycin substituted for the 3'-terminal adenine. As judged from differential UV absorbance melting curves the formycin label had virtually no influence on the conformation of the tRNA. A temperature jump apparatus was modified to allow the simultaneous observation of transmission and fluorescence intensities by two independent optical channels. The design of a temperature jump cell with an all quartz center piece is given. The cell is resistant to temperatures up to 90 degrees C; it provides high optical sensitivity, low stray light intensity and the possibility of measuring fluorescence polarization. The T-jump experiments allowed to discriminate between fast unspecific fluorescence quenching (r less than 5 musec) and slow cooperative conformational changes. In the central part of the temperature range of UV-melting (midpoint temperature 30 degrees C in 0.01 M Na+ and 39 degrees C in 0.03 M Na+, pH 6.8) two resolvable relaxation processes were observed. The corresponding relaxation times were 20 msec and 800 msec at 30 degrees C in 0.01 M Na+, and 4 msec and 120 msec at 39 degrees C in 0.03 M Na+. The Y-base fluorescence shows both of the relaxation effects, which almost cancel in equilibrium fluorescence melting, because their amplitudes have opposite signs. From this finding the existence of some residual tertiary structure is inferred which persists after the unfolding of the main part of tertiary structure during early melting (midpoint temperature 24 degrees C in 0.03 M Na+). In the fluorescence signal of the formycin also the two relaxation effects appear. Both of them are connected with a decrease of the fluorescence intensity. From the results a coupled opening of the anticodon and acceptor branches is concluded.

Adenine↗