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Biomedical subjects

J Brahms

Publications and source records attributed to J Brahms.

At least 19 recordsLinked to original sources
PubMed1989

The synthetic DNA duplex of poly d(Abr5U).poly d(Abr5U) adopts an A-DNA-like structure.

An X-ray fiber diffraction study of the synthetic DNA duplex poly d(Abr5U).poly d(Abr5U) shows that its sodium salt adopts an unexceptional A-DNA-like structure. Similar to A-DNA, two molecules are packed in a monoclinic unit cell (a = 2.23 nm, b = 4.14 nm, c = 5.61 nm and alpha = beta = gamma = 90 degrees) of space group C2. Because of its dinucleotide chemical motif, the c-repeat is twice that in A-DNA but, notably, corresponding backbone conformation angles of adjacent nucleotides are almost identical. This is in marked contrast to many B-like conformations of polydinucleotides.

Crystallization↗
PubMed1983

Conformational transitions in the synthetic polynucleotide poly[d(G-C)] . poly[d(G-C)] double-helix.

Conditions are described for observing by X-ray fibre diffraction the A, B and S conformations of the poly[d(G-C)] . poly[d(G-C)] double-helix and also a new form designated as B". For fibres with an appropriate ionic content, transitions between these conformations can be induced by varying the relative humidity of the fibre environment. With increasing relative humidity the transitions B" leads to A leads to S leads to B occur. However, reducing the relative humidity does not result in a simple reversal of these transitions. If the relative humidity is reduced rapidly, a B leads to A transition is observed followed by an A leads to B" transition, but if it is reduced slowly, the transition is from B to S. Once the S form has been assumed, further reduction in the relative humidity does not result in a transition to the A form. The S form emerges as a particularly stable form of the poly[d(G-C)] . poly[d(G-C)] double-helix. From the point of view of its relationship to the classical A and B forms, the S form of poly[d(G-C)] . poly[d(G-C)] is shown to exhibit similarities to the D form of poly[d(A-T)] . poly[d(A-T)].

Humidity↗
PubMed1983

Conformational transitions in oriented fibres of the synthetic polynucleotide poly[d(AT)].poly[d(AT)] double helix.

The synthetic polynucleotide poly[d(AT)].poly[d(AT)] is of interest in studies of the relationship between nucleic acid structure and function. In particular, A + T-rich regions in DNA double helices have been invoked as centres for controlling the transcription of genetic information. Here we describe conditions for observing by X-ray fibre diffraction the A, B, C and D conformations of Na-poly[d(AT)].poly[d(AT)], and for inducing transitions between these conformations. The D form emerges as a particularly stable conformation; once assumed, it persists over a wide range of variation in the relative humidity of the fibre environment. Further, while transitions between the B and D conformations are readily reversible, transitions between A and D are much more complex.

Nucleic Acid Conformation↗
PubMed1980

Site and role of the N-terminal fragment of the nucleosomal core histones in their binding to deoxyribonucleic acid as determined by vibrational spectroscopy.

The site and role of the binding of the 1-53 N-terminal part of H4 on DNA have been studied by optical spectroscopy. The structure of the 1-53 H4 fragment determined by vacuum ultraviolet circular dichroism and infrared spectroscopy is essentially aperiodic. The site of the interacion between the fragment and free DNA is localized by Raman laser spectroscopy in the small groove of the DNA, similar to the interaction site of the whole histone with DNA in nucleosomes. Infrared linear dichroism measurements show that the two 1-53 and 54-102 H4 fragments play a very important role in the histone-DNA interactions, but the roles are extremely different: the N-terminal part of the histone remains effectless on the DNA conformational flexibility and it is proposed that the structurally important interaction occurs between the globular part of the histone and the DNA. The N-terminal fragment appears to be responsible for finding the correct place on the DNA of the nucleosomal core particles.

Amino Acid Sequence↗
PubMed1979

Effect of 5-alkyl substitution of uracil on the thermal stability of poly [d(A-r5U)] copolymers.

The thermal transition of poly[d(A-r5U)] polydeoxynucleotides (where r was a hydrogen atom, or a methyl, ethyl, n-propyl, n-butyl or n-pentyl group) was studied by measuring the derivative melting profiles of the polymers in the range of 0.01--0.36 M K+, at pH 6.8. According to the Tm values, polydeoxynucleotide analogues show lower thermal stability than poly[d(A-T)] at any counterion concentration applied. At a given salt concentration, Tm of the alkyl analogues decreased as the number of carbon atoms (n) in the r substituent of poly[d(A-r5U)] increased. 1/Tm plotted against against 1/n yielded a linear relationship. Cooperativity of the melting of all poly[d(A--U)] analogues decreased with the increase of salt concentration in the solution. This change depended again on 5-substitution of the uracil moiety of poly[d(A-U)]. Smallest decrease was observed in the case of poly[d(A--U)] whereas largest decrease was shown by poly[d(A-pe5U)] (pe=pentyl group).

Alkylation↗
PubMed1978

Form of DNA and the nature of interactions with proteins in chromatin.

Studies of native chromatins and of isolated nucleosomes (from calf thymus) show that the DNA is in the B form or modified B form. This was determined by Raman spectroscopy of chromatins, of nucleosomes (from calf thymus) and of DNA fibres and directly correlated with X-ray diffraction studies. The Raman spectra of three forms of DNA (A, B and C) have been characterized in fibres both by X-ray diffraction and Raman spectroscopy on the same sample. In particular, the Raman spectrum of the C form of DNA is characterized by a band of about 870 cm(-1). For the first time, chromatins of different origins with increasing content of non-histone proteins have been investigated by Raman spectroscopy. The site of interaction of the non-histone proteins appears to involve the N7 position of guanine while the histone core does not interact at this site. It is proposed that the mechanism of specific recognition in chromatin involves the large groove.

Animals↗
PubMed1978

Subunit topography of RNA polymerase (E. coli) in the complex with DNA.

E. Coli RNA polymerase binding to different DNAs (from E. Coli, 5-bromodeoxyuridine (BrdUrd) substituted DNA and poly [d(BrU-A)] was induced with ultraviolet (U.V.) light to form protein-DNA crosslinked complexes. Two independent methods of analysis, polyacrylamide gel electrophoresis in SDS and chloroform extraction indicated the formation of a stable complex between the enzyme and DNA. The complexes were formed under different ionic strength conditions, at low enzyme to DNA ratios in order to approach the conditions of specific binding. In contrast there was no crosslinking of the complex in 1 M KCl solution which dissociates the enzyme from DNA. The efficiency of formation of strongly bound complex was found to be much higher with holoenzyme than with core enzyme. The following results were obtained : 1) The large subunits beta and beta' were found to be bound to DNA. 2) Relatively small amount of sigma subunit were bound to DNA while alpha subunits were essentially not attached to DNA. The high binding affinity of beta and beta' subunits was also observed in the studies of isolated subunits. These results lead to a model of enzyme-DNA complex in which the large beta and beta' subunits provide the contacts between the RNA polymerase and the DNA.

Bromodeoxyuridine↗
PubMed1977

Infrared linear dichroism investigations of deoxyribonucleic complexes with histones H2B and H3.

Complexes between DNA and histones H2B and H3 were studies by means of infrared linear dichroism in a wide range of histone to DNA ratios and of different relative humidities. The measurement of the dichroic ratios allows one to determine the secondary structure of DNA in the complexes. It is shown that the progressive addition of histone H2B or H3 to DNA inhibits the structural B leads to A transition and DNA remains in a B-type form at low relative humidity. A new simple method is proposed to evaluate the amount of A or B forms of DNA when both structures are present. It is found that the B leads to A transition is fully inhibited when only one molecule of H2B or H3 histone is bound per about three or four turns of DNA helix, respectively. It is proposed that about four to three turns of DNA helix represent the "critical length of DNA" (minimum "cooperative unit") for the B leads to A transition.

Animals↗
PubMed1977

Identification of beta,beta-turns and unordered conformations in polypeptide chains by vacuum ultraviolet circular dichroism.

Different conformations of polypeptides were characterized by measurements of the circular dichroism (CD) extended into the vacuum ultraviolet region. (i) The linear beta-pleated sheet structure was characterized in a broad ultraviolet region down to 165 nm by examination of copolypeptides composed of alternating hydrophobic and hydrophilic amino-acid residues, e.g., poly(Lys-Leu-Lys-Leu). A short-wavelength intense band was found at about 169 nm, which is characteristic of beta-pleated sheet conformation. (ii) The beta-turns were experimentally measured using poly(Ala(2)-Gly(2)) in a broad spectral region down to 165 nm with accuracy. The observed CD spectrum is in excellent qualitative agreement with the theoretical curve calculated by Woody for the beta-turns of type II and/or I of Venkatachalam. The similarity in shape between the theoretical curve and the observed CD spectra suggests a dominance of beta-turn segments in the poly(Ala(2)-Gly(2)) structure. The presence of beta-turns in poly(Ala(2)-Gly(2)) is also in agreement with the characterization of this polypeptide by solid state methods (electron microscopy and x-ray diffraction). The CD spectrum of beta-turns is characterized by a very intense band at 207.5 nm and strong negative bands at 191 and 169 nm. Copolypeptides such as poly(Ala(2)-Gly(3)) and poly(Ala(3)-Gly(3)) yielded a similar type of CD spectrum, analysis of which indicates that a large fraction of their residues is contained in beta-turn regions. (iii) The CD spectrum of the unordered chain of these alternating copolypeptides in salt-free solution is observed in the vacuum ultraviolet region.

Circular Dichroism↗
PubMed1977

Effect of non-histone proteins on thermal transition of chromatin and of DNA.

The effect of chromatin non-histone protein on DNA and chromatin stability is investigated by differential thermal denaturation method. 1) Chromatin (rat liver) yields a multiphasic melting profile. The major part of the melting curve of this chromatin is situated at temperatures higher than pure DNA, with a distinct contribution due to nucleosomes melting. A minor part melts at temperatures lower than DNA which may be assigned to chromatin non-histone protein-DNA complex which destabilized DNA structure. 2) Heparin which extracts histones lowers the melting profile of chromatin and one observes also a contribution with a Tm lower that of pure DNA. In contrast, extraction on non-histone proteins by urea supresses the low Tm peak. 3) Reconstitution of chromatin non-histone protein-DNA complexes confirms the existence of a fraction of chromatin non-histone protein which lowers the melting temperature when compared to pure DNA. It is concluded that chromatin non-histone proteins contain different fractions of proteins which are causing stabilizing and destabilizing effect on DNA structure.

Animals↗
PubMed1976

Nature of conformational changes in poly[d(A-T)-d(A-T)] in the premelting region.

The conformation of the synthetic DNA, poly-[d(A-T)-d(A-T)], has been investigated both in the solid state and in dilute aqueous solutions at different temperatures below its melting point. The change of the circular dichroism (CD) spectra of poly[d(A-T)-d(A-T)] solutions with decreasing temperatures from just below the melting point to 0 degrees involves a specific decrease of the intensity of the 262 nm CD band. This conformational change has been assigned to a gradual and partial transition from the B to C form, on the basis of the following results: (i) By the use of infrared dichroism measurements on oriented films we have defined humidity and salt conditions under which B and C forms of poly[d(A-T)-d(A-T](Li+) are stable. In addition, we find that ammonium salts induce the C form of poly[d(A-T)-d(A-T)] even at high relative humidity. (ii) CD studies of the films of the lithium salt of poly[d(A-T)-d(A-T)] under the same conditions have given CD spectra corresponding to the B and C forms of this polynucleotide. In addition, the CD spectrum of the ammonium salt of poly[d(A-T)-d(A-T)] in solution approaches that of the C form in films. (iii) The conformational change of poly[d(A-T)-d(A-T)] as a function of temperature can be entirely explained on the basis of changes in the double-stranded base-paired structure. Our data rule out hydrogen bond breaking and unstacking or "breathing" as an explanation of the premelting changes. Curves of the continuous variation of CD(epsilon at 262 nm) as a function of temperature (from 0 degrees to the melting zone) show similar slopes in the presence of different agents stabilizing the double-stranded structure, such as Mg++, or at different salt concentration (KCl), indicating that the nature of the process is independent of ionic strength. Some specific effects were observed in the influence of certain neutral salts; ammonium induces the C form whereas magnesium favors the B form. CD data give direct evidence that a DNA like poly[d(A-T)-d(A-T)] need not change conformation upon transition from a dilute aqueous solution to a highly hydrated (film/gel) solid state. The change of conformation begins only at a defined partial dehydration.

Circular Dichroism↗