[STUDIES ON NUCLEIC ACIDS. XI. ISOLATION OF DESOXYRIBONUCLEIC ACID FROM MICROORGANISMS IN PURE, HIGH MOLECULAR FORM]

DNA interaction of the imidazole-containing lexitropsin ImPy: titration viscometric study in comparison to netropsin

The imidazole (Im) containing lexitropsin ImPy related to netropsin (Nt) is a sequence reading DNA ligand which, in contrast to Nt, permits binding to a GC base pair. The ImPy induced DNA conformational changes differ significantly from those induced by Nt as monitored by titration viscometry, although interaction modes have also been resolved with boundaries at the same ligand to DNA phosphate ratio, r. Evidently ImPy covers similar binding sites (in the same sequence) as Nt for natural calf thymus DNA at r < 0.023. This result suggests that the preferred binding sites of ImPy are A tracts (cf. K.E.R. JBSD 9(1993) 973), in agreement with previous data. The respective DNA coil expansion, most probably caused by unbending (l.c.), is similar but smaller compared to the Nt-DNA interaction. These results again suggest that, at low r values, the van der Waals interaction in the narrowed minor groove of AT clusters provides a dominating energy contribution to ImPy binding. At r > 0.03 the DNA coil expansion increases to extremely high values in that r range where Nt binding (to mixed AT/GC sequences) induces no effect at all owing to steric hindrance with the amino group of guanine. On the basis of many quantitative results for the Nt-DNA systems these effects can be understood in terms of an unbending of intrinsic helix bends (l.c.). They are of considerable interest in connection with the ability of such compounds to influence the direction of the local regulatory relevant DNA curvature.

Eukaryotic DNAs in solution contain characteristic components of tertiary structure

For natural eukaryotic DNA in solution, we suggest the existence of secondary-helix components superponed to parts of the DNA double helices. In a previous report we found, for calf thymus DNA in solution and of different mean molar mass Mr, an electrostatically driven rise of the hydrodynamically operative contour length of the double helix. This result was derived from Mr-dependent systematic deviations from the almost but not exactly linear plots of intrinsic viscosity [eta] as a function of 1/cs1/2 (cs = Na+ concentration) accurately determined by a titration technique [K.G. and K.E.R., Nucl. Acids Res. 8, 2807 (1980)]. In order to discriminate between DNA elongation contributions caused by secondary or by tertiary structure effects, respective measurements have now been extended to different temperatures for two eukaryotic and two prokaryotic DNA species. The slope of the curves obtained for the (apparent) gradual elongation effect as a function of temperature is negative for the eukaryotic DNAs investigated and is smaller and positive for the prokaryotic species, thus revealing different underlying main elongation mechanisms. We propose that, for the eukaryotic DNA samples, an electrostatically driven partial abolition of tertiary structure components is responsible for the prevailing part of the DNA elongation effect measured. (A helix elongation of this type may be the result of an abolition of an apparent helix shortening as realized in a very high degree on formation of nucleosome chains or in a less degree by DNA molecules with a respective evolutionarily fitted tertiary structure). For the smaller effects of prokaryotic DNA species something like a base breathing seems to dominate. Recent literature results support such an interpretation.

Interaction of anthracycline antibiotics with biopolymers: comparative studies of DNA binding and antimicrobial activity of rhodomycin-type anthracycline antibiotics

The binding of the anthracyclines beta-rhodomycin-I and beta-rhodomycin-II to calf thymus DNA was investigated by both equilibrium and kinetic methods taking into account ligand dimerization (ionic strength I = 0.2 M, pH 6.0). The analysis was based upon a cooperative single-step binding mechanism with overlapping of potential binding sites on a linear homogeneous lattice. Equilibrium binding parameters were estimated from spectrophotometric titration experiments by means of a nonlinear fitting program. The results were compared with those obtained previously for the related antibiotic iremycin and were complemented by kinetic parameters determined from temperature-jump experiments at high binding ratio. The binding constants and the mean attachment times of the drugs were found to increase in the serial order iremycin, beta-rhodomycin-I and beta-rhodomycin-II, which is in line with their increasing antimicrobial activity on Bacillus subtilis ATCC 6633.

Counterion dependent variation of DNA secondary structure in (A . T) clusters: evidence by use of netropsin as a structural probe

The interaction of the oligopeptide antibiotic netropsin (Nt) with (A . T) regions of DNA is characterized by a spectrum of discrete modes. This has been revealed by viscometric analysis, at 20 degrees C and 0.2 M "counterions", for NaDNA in a preceding and for NH4DNA in this paper. The increase of DNA contour length as induced by one Nt molecule was found to depend on the special mode only, while the respective stiffening is generally higher for NH4DNA. The latter property is interpreted in terms of an enhanced flexibility, relative to that of NaDNA, of the (A . T) cluster segments before complex formation. For some of the interaction modes of the DNA-Nt systems a difference in the number of corresponding binding sites has been observed. This phenomenon is understood by assuming an influence of the counterion species upon existing equilibria between different forms of the (A . T) cluster secondary structure. Not less than 5 to 10% of the total DNA are effected in this manner. Upper limits for the local differences in the axial rise per base pair are 0.04 nm and 0.02 nm.

Immunochemical detection of N6-methyladenine in DNA

Antibodies to N6-methyladenosine were produced in rabbit by means of immunization with N6-methyladenosine coupled to bovine serum albumin via periodate oxidation. Cross-reacting antibodies were removed by bovine serum albumin-Sepharose and appropriate nucleoside-human serum albumin absorbents. Nucleoside-specific antibodies were isolated by affinity chromatography of N6-methyladenosine-human serum albumin-Sepharose. The specificity of the purified antibodies has been demonstrated by complement fixation inhibition analyses using nucleoside analogues as inhibition than dAMP. Anti-N6-methyladenosine was used to detect N6-methyladenine in denatured DNAs from various sources by complement fixation. Practically no complement fixation has been found with DNAs containing no N6-methyladenine, such as calf thymus, salmon sperm, Micrococcus radiodurans, Streptomyces chrysomallus and Streptomyces hygroscopicus, whereas a weak reactivity occurred in the case of Bacillus subtilis DNA and Sarcina maxima DNA. For DNA from Proteus mirabilis, Escherichia coli K-12, E. coli B, E. coli WF+, lambda, T2 phages quantitative differences in the immunochemical reactivity were observed, which only partially correlate with the N6-methyladenine content of the DNAs. Other factors, influencing the accessibility of N6-methyladenine to the antibody-combining site have to be taken into consideration.

Basic polypeptides as histone models. Effect of conformation, base composition and methylation of nucleic acids on the interaction with H1 and histone models and on the circular dichroism of complexes

Interaction of histone H 1 and models simulating histone chains was followed by monitoring the melting curves of supernatants after the sedimentation of aggregated complexes. In a mixture of two DNAs the histones reacted selectively with (A+T)-rich and non-methylated DNA, respectively. H 1 and (Ala-Lys-Pro)n also interacted preferentially with DNA in a mixture with double stranded RNA whereas (Lys30,Ala70)n did not show any selectivity. (G+C)-rich DNA in complexes showed CD spectra the intensity of which decreased with increasing DNA methylation to values comparable with these of complexes of (A+T)-rich DNA. In complexed with double stranded RNA only the polymer (Lys30,Ala70) displayed CD pattern similar to spectra of complexes with DNA. It was concluded that formation and structure of complexes depend selectively on the DNA conformation and base composition.

Der einfluss von coffein auf das schmelzverhalten von DNS

The interaction of caffeine with DNA has been studied at several ionic strengths by heat denaturation. At 2 mM K(+) caffeine produces a stabilization, but at 20 mM K(+) or higher a destabilization of secondary structure of DNA occurs. There is a correlation between heterogeneity and destabilization of DNA in presence of caffeine. In the premelting region a hyperchromic effect can be observed. It is suggested that two binding processes exists in the DNA-caffeine interaction.

Optical rotatory dispersion properties of nucleic acid complexes with the oligopeptide antibiotics distamycin A and netropsin

ORD measurements of nucleic acids in the presence of the oligopeptides netropsin and distamycin A have indicated association of the antibiotics with DNA and strong conformational changes of the DNA structure with specificity to AT-rich helical regions. The RNA conformation is relatively unaffected by these antibiotics. The results are explained in terms of a perturbation of the DNA secondary structure as well as of the chromophore system of the oligopeptides.

Effect of distamycin a on the structure and template activity of DNA in RNA - polymerase system

It is shown that native and denatured DNA form complexes with the oligopeptide-antibiotic distamycin A. The pronounced inhibition of the incorporation of AMP into RNA in the DNA directed RNA-polymerase system is due to the interference of the antibiotic with DNA.