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A Rupprecht

Publications and source records attributed to A Rupprecht.

At least 37 records · Page 2Linked to original sources
PubMed1994

A mechanochemical study of MgDNA fibers in ethanol-water solutions.

Highly oriented calf-thymus MgDNA fibers, prepared by a wet spinning method, were studied with a simple mechanochemical set-up. The relative fiber length, L/Lo, was measured with the fibers submerged in ethanol-water solutions. In one type of experiment L/Lo was measured as a function of ethanol concentration at room temperature. No substantial decrease in L/Lo with increasing ethanol concentration was observed, indicating that MgDNA fibers stay in the B form even when the water activity is very low. For low ethanol concentrations the fiber structure is stable and does not dissolve even at very high water activities. In a second type of experiment, the heat-induced helix-coil transition was manifested by a marked contraction of the fibers. The transition temperature decreases linearly with increasing ethanol concentration between 52 and 68% ethanol. At higher ethanol concentrations the helix-coil transition temperature increases due to strong aggregation within the DNA fibers, and above 77% ethanol the fibers do not contract at all, not even at the upper temperature limit of the experiments, approximately 80 degrees C. This behavior is discussed with reference to dried DNA and the P form of DNA. The helix-coil transition temperature of the MgDNA fibers in 70% ethanol does not show any dependence on the MgCl2 concentration. It is shown that the Poisson-Boltzmann cylindrical cell model can account qualitatively for this lack of salt dependence.

Animals↗
PubMed1994

Optical properties of CsDNA films as a function of hydration.

The refractive indices of wet-spun films of CsDNA have been measured for light polarized parallel and perpendicular to the helical axis as a function of relative humidity (RH). These data have been combined with previously published data (Biopolymers 30 (1990) 877-887) for the volume per base pair and water content as a function of RH in order to extract the optical polarizabilities. This work was motivated by the study of Weidlich et al. (Biopolymers 26 (1987) 439-453) who reported a approximately 35% increase at the A-to-B transition in the parallel and perpendicular polarizabilities of NaDNA. In contrast, a much smaller increase in the polarizabilities of CsDNA is found near the A-to-B transition: approximately 12% for the perpendicular direction and < or = 4% for the parallel direction.

Anisotropy↗
PubMed1994

Free radicals from oriented DNA fibers after irradiation at 77 K: continuous-wave and pulsed electron paramagnetic resonance spectroscopy from D2O-equilibrated specimens.

Combined continuous-wave and field-sweep electron spin echo spectroscopy was employed to unravel the components of the spectra in oriented DNA fibers equilibrated in 76% relative humidity of D2O vapor formed upon X irradiation at 77 K and stabilized at that temperature. Using DNAs with different counter-ions (Na+, Li+, Cs+), different base composition (calf thymus, Cl. perfringens), substituted thymine bases (deuterated thymine, 5-halouracil substitution) as well as the copolymer poly(A:U), nine different components were discerned. The spectra of two components, known before partially, were fully characterized. One of them should probably be associated with a cytosine anion, the other with a guanine cation, the latter connection having already been made in previous work. A third component, invoked previously from work with DNA containing deuterated thymine, was also fully characterized and could be assigned to a thymine anion. For one of the new components, an assignment to the allyl radical, probably on the thymine base, could be given on account of the characteristics of the spectra. Tentative assignments are given for three other components which involve an anion on the adenine and the guanine base, respectively, as well as an oxidation-derived species comprising a glycosidic nitrogen, perhaps on cytosine.

Animals↗
PubMed1993

Optical third harmonic generation study of the hydration of DNA films.

Optical third harmonic generation (THG) has been observed for the first time from DNA films. The THG signal is observed from NaDNA films exposed to relative humidities (RHs) between 0% and 98%. A strong enhancement (approximately 5x) of the THG signal from NaDNA is observed at 84% RH; no enhancement is observed for RbDNA. The most likely mechanism for such an enhancement is an increased coherence length. A model calculation using estimates of the refractive indices at both the fundamental and third harmonic frequencies supports this interpretation. The observed THG signal has the same polarization as the incident (fundamental) light. For the A conformation, the THG signal polarized perpendicular to the helical axis is approximately twice as strong as the signal polarized parallel to the helical axis. No such anisotropy is observed for either the disordered conformation (below about 50% RH) or the B conformation (above 92% RH).

Biophysics↗
PubMed1993

Raman and infrared studies of wet-spun films of Na-hyaluronate.

Raman and infrared (IR) studies of Na-hyaluronate films have been performed as a function of relative humidity (RH) and temperature. These data show a number of vibrational modes. Certain of these modes are evident in both the Raman and IR data. Changes in the Raman spectra are observed at the order-disorder phase transition (between 84 and 90% RH) and suggest that the molecular conformation changes at the phase transition.

Carbohydrate Conformation↗
PubMed1992

The formation of A-DNA in NaDNA films is suppressed by netropsin.

Oriented films of NaDNA complexed with netropsin were studied with deuterium nuclear magnetic resonance (2H NMR), X-ray diffraction and ultraviolet (UV) linear dichroism to obtain information about the influence of netropsin on the structural arrangement of the DNA bases and on the B-A transition. The results of these studies clearly demonstrate a strong suppression of the formation of A-DNA at relative humidities (RHs) down to about 50%. The suppression was complete in the NaDNA-netropsin complex studied with 2H NMR which had a netropsin input ratio, r, of 0.22 drug/base pair. The sample used for UV linear dichroism had a similar input ratio while the X-ray diffraction samples had input ratios between 0.033 and 0.39 drug/base pair. Together, the results of these studies are in agreement with previous infrared (IR) linear dichroism studies of the conformation of the sugar-phosphate backbone in NaDNA-netropsin complexes, which showed that the B-A transition is suppressed for r-values down to approximately 0.1 drug/base pair (Fritzsche, H., Rupprecht, A. and Richter, M., Nucleic Acids Res. 12 (1984) 9165-9177).

Animals↗
PubMed1992

A study of the quadrupolar NMR splittings of 7Li+, 23Na+, and 133Cs+ counterions in macroscopically oriented DNA fibers.

The hydration and temperature dependencies of the 23Na+, 133Cs+, and 7Li+ quadrupolar splitting have been determined in hydrated, macroscopically oriented DNA fibers. At low water contents the quadrupolar splitting is found to decrease as the water content increases, regardless of counterion, while at high water contents the hydration dependence is reversed. The 23Na+ and 133Cs+ quadrupolar splittings decrease as the temperature increases, while the 7Li+ splitting shows the opposite behavior. At high water contents the 23Na+ and 133Cs+ splittings decrease, and then, after passing zero splitting, increase as the temperature increases. The interpretation of the temperature dependence is discussed in terms of a two-site model (free and bound ions) and a three-site model (free ions and specifically or nonspecifically bound ions). It is suggested that a three-site model is more consistent with the data for the present system. At high water contents, the temperature dependence of the 7Li+ splitting vanishes, indicating counterion condensation. The behavior of the 7Li+ splitting is confirmed by measurements on DNA fibers in equilibrium with a C2H5OD-D2O-LiCl solution. The salt dependence in this system is weak. The counterion quadrupolar splitting is seen to be very sensitive to structural transitions in double-helical DNA.

Animals↗
PubMed1992

Optical and physical properties of wet-spun films of Na-hyaluronate. Evidence of a phase transition.

The refractive indices, water content, and volume of wet-spun films of Na-hyaluronate have been measured as a function of relative humidity (rh). These data are used with the Lorentz-Lorenz formula to determine the optical polarizabilities of Na-hyaluronate parallel and perpendicular to the helical axis. The analysis reveals a drop in the optical polarizabilities of approximately 20% between 80 and 88% rh, indicating a phase transition.

Carbohydrate Conformation↗
PubMed1991

NMR spin grouping and correlation exchange analysis. Application to low hydration NaDNA paracrystals.

The NMR spin-grouping technique is applied to low hydration oriented fibers of NaDNA to study the role of exchange in determining the apparent (observed) spin relaxation of the system. The analysis proceeds in three steps: first, the apparent proton relaxation is measured at high fields, with both selective and nonselective inversion pulse sequences, and in the rotating frame. The spin-grouping technique is used in all spin-lattice relaxation measurements to provide the optimum apparent relaxation characterization of the sample. Next, all apparent results are analyzed for exchange. In this analysis the results from the high field and rotating frame experiments (which probe the exchange at two different time scales) are correlated to determine the inherent (or true) spin relaxation parameters of each of the proton groups in the system. The results of selective inversion T1 measurements are also incorporated into the exchange analysis. Finally, the dynamics of each spin group are inferred from the inherent relaxation characterization. The low hydration NaDNA structure is such that the exchange between the protons on the water and those on the NaDNA is limited, a priori, to dipolar mixing. The results of the exchange analysis indicate that the dipolar mixing between water and NaDNA protons is faster than the spin diffusion within the NaDNA proton group itself. The spin-diffusion on the macromolecule is the bottleneck for the exchange between the water protons and the NaDNA protons. The water protons serve as the relaxation sink both at high fields and in the rotating frame for the total NaDNA-water spin bath. The inherent relaxation of the water is characteristic of water undergoing anisotropic motion with a fast reorientational correlation time about one axis (5 X 10(-10) less than or equal to tau r less than or equal to 8 X 10(-9)S) which is about three orders of magnitude slower than that of water in the bulk; and a slow tumbling correlation time for this axis (1.5 x 10(-7) less than or equal to tau t less than or equal to 8 x 10(-7)S) which is two orders of magnitude slower yet.

Crystallography↗
PubMed1990

Deuterium relaxation and internal motion in solid Li-DNA.

As part of an effort to explore the nature of the internal motion in solid polynucleotides, the spectral densities of motion J1(omega 0) and J2(2 omega 0) have been measured for oriented, partially hydrated samples of calf thymus Li-DNA deuterated in the guanine and adenine 8-positions. Both spectral densities increase with increasing hydration level, J1 is found to be 2-5 times larger than J2, and their frequency dependence appears to be omega-1 and omega-3/2, respectively. The large values of the ratio J1/J2 rule out any in-plane torsional motion as the dominant relaxation mechanism in these samples, but a drop in this ratio at high hydration levels (G13 H2O/nucleotide) may indicate increasing contributions from such torsional motion. Although a satisfactory fit to a particular motional model has yet to be achieved, our findings show that the librational motion of the C8-D bond at or below a hydration level of 10 H2O/nucleotide is approximately uniaxial, with correlation times for the motion in the range 0.2-3.0 microseconds.

DNA↗
PubMed1990

Counterion effects on the physical properties and the A to B transition of calf-thymus DNA films.

We report measurements of the water content and swelling of wet-spun films of Na-, K-, Rb-, and Cs-DNA as a function of relative humidity (rh). The water contents (number of water molecules per base pair of DNA) of these films are found to be quite similar, indicating that the identity of the counterion species is unimportant for the water content. Since the A to B transition for these DNAs occurs at different rhs, the corresponding water contents of the A to B transition are found to be quite different. These films swell as a function of rh in a very similar manner, implying that the changes in the intermolecular bonds in the different DNAs are similar. Dramatic changes are observed in the dimensions of the films above 84% rh for all types of DNA. Combining the water content and swelling measurements yields the dependence of the volume per base pair on water content. The volume per base pair is observed to be a nonlinear function of water content, indicating nonideal mixing of the water with the DNA.

Animals↗
PubMed1990

A Raman study of low frequency intrahelical modes in A-, B-, and C-DNA.

We have obtained low frequency (less than 200 cm-1) Raman spectra of calf-thymus DNA and poly(rI).poly(rC) as a function of water content and counterion species and of d(GGTATACC)2 and d(CGCGAATTCGCG)2 crystals. We have found that the Raman scattering from water in the first and second hydration shells does not contribute directly to the Raman spectra of DNA. We have determined the number of strong Raman active modes by comparing spectra for different sample orientations and polarizations and by obtaining fits to the spectra. We have found at least five Raman active modes in the spectra of A- and B-DNA. The frequencies of the modes above 40 cm-1 do not vary with counterion species, and there are only relatively small changes upon hydration. These modes are, therefore, almost completely internal. The mode near 34 cm-1 in A-DNA is mostly internal, whereas the mode near 25 cm-1 is dominated by interhelical interactions. The observed intensity changes upon dehydration were found to be due to the decrease in interhelical distance. Polymer length appears to play a role in the lowest frequency modes.

Base Sequence↗
PubMed1990

Modulation of the B-A transition of DNA by potential antitumor antibiotics. Influence of the base composition of DNA.

The B-A transition of DNA in oriented films of DNA-drug complexes is more or less restricted as a consequence of drug binding as revealed by infrared linear dichroism. A fraction of DNA is irreversibly locked into the B form. This behavior is described by the number of DNA base pairs "frozen" in the B form by one drug molecule. This quantity is dependent on the DNA sequence the drug is attached to. In this paper, drug complexes of oriented films of NaDNA with a GC content of 42% from calf thymus and a GC-rich DNA from Micrococcus lysodeikticus were compared. The restriction of the B-A transition of DNA complexes with two intercalating antibiotics, aclacinomycin A and violamycin BI, is not severely influenced by the base composition of DNA. By contrast, the strong groove binding oligopeptide antibiotics netropsin and distamycin A are much less effective to restrict the B-A transition of GC-rich DNA than of AT-rich DNA. This finding is in agreement with previous results by other methods which support a model based upon a strong preference of AT clusters by these two non-intercalating drugs.

Antibiotics, Antineoplastic↗
PubMed1989

Structure of DNA hydration shells studied by Raman spectroscopy.

We have used Raman scattering to study the water O-H stretching modes at approximately 3450 and approximately 3220 cm-1 in DNA films as a function of relative humidity (r.h.). The intensity of the 3220-cm-1 band vanishes as the r.h. is decreased from 98% to around 80%, which indicates that the hydrogen-bond network of water is disrupted in the primary hydration shell (which therefore cannot have an "ice-like" structure). The number of water molecules in the primary hydration shell was determined from the intensity of the approximately 3200-cm-1 band as about 30 water molecules per nucleotide pair. The approximately 3400-cm-1 O-H stretch band was used for determining the total water content, and this band persists at 0% r.h., implying that 5-6 tightly bound water molecules per nucleotide pair remain. The frequency of the approximately 3400-cm-1 O-H stretch mode is lower by 30 to 45 cm-1 in the primary hydration shell compared to free water. The water content as a function of r.h. obtained from these experiments agrees with gravimetric measurements. The disappearance of the approximately 3200-cm-1 band and the shift of the approximately 3400-cm-1 O-H stretch band provide a reliable way of measuring the hydration number of DNA.

DNA↗
PubMed1989

Hydration structure in natural DNA observed by thermal neutron scattering.

Films of highly oriented Na- and LiDNA showing the typical X-ray diffraction patterns for the A-, B-, and C-conformation have been investigated by elastic and quasielastic neutron scattering. Information concerning the question of the DNA-water interaction has been obtained by varying the parameters H2O/D2O contrast, humidity, and temperature. Main observations are: A coexistence of one- and three-dimensionally correlated DNA which shifts towards the one-dimensionally correlated C-conformation for high humidity; a coexistence of A-, B-, and C-conformation for NaDNA with a similar humidity dependence; a factor of two increase between the average degree of localization of water hydrogens compared with DNA hydrogens at 75% r.h. for NaDNA; a strong water contribution to layer peaks which are close to the susceptibility maximum of water; a strong temperature dependence of the axial repeat distance for C-DNA; broad quasielastic spectra around the inverse of this distance. The observations are interpreted in terms of a competition between finite three-dimensional correlation and an optimized spatial resonance of nearly one-dimensionally correlated DNA with the correlation of bulk water. The observations are compatible with the concept of water spine formation (Dickerson 1983). The interpretation emphasizes the dynamic character of this mechanism in the region of nearly one-dimensionally correlated DNA.

DNA↗