The formation of Antiparallel-Parallel-Combination (APC) DNA, a liner duplex with a segment of parallel-stranded (ps) helix flanked by conventional B-DNA, was tested with a number of synthetic oligonucleotides. The groove-binding ligand distamycin A (DstA) was used to stabilize the ps segment comprising five A x T base pairs. Two drug molecules bound per APC, one in each of the two equivalent grooves characteristic of ps-DNA.
View Article and Find Full Text PDFThe transition of the 14-meric deoxyoligonucleotide duplex d-(ACCCCCTTTTTTTG).d-(CAAAAAAAGGGGGT) from the B- to the A-conformation in water/trifluorethanol (TFE) solution was studied with the use of circular dichroism. An increase in the fraction of TFE induces a two-step B-A transition.
View Article and Find Full Text PDFThe consensus DNA sequence for binding of the Escherichia coli cyclic AMP receptor protein (CRP) has two symmetrically related inverted recognition elements TGTGA:TCACA, separated by a variable spacer, normally 6 bp long. We have shown that the CRP-cAMP complex, when bound to synthetic binding sites with an extended 8 bp spacer segment, induces an increase in the DNA circular dichroism (CD). The CD change at lambda > 275 nm agrees with the shift of approximately one helical turn of DNA into A-like form.
View Article and Find Full Text PDFOnly recently first direct evidence for the involvement of the A-DNA in the biological processes and structures has been obtained. This was preceded by numerous studies during four decades, which revealed structural features of this second, next to the B-form, DNA conformation, the conditions for the B to A transition to occur in a tube, the requirements to nucleotide sequence. Due to these works the B-A cooperative transition in DNA is now understood as good as the DNA melting.
View Article and Find Full Text PDFSelf-complementary oligodeoxynucleotides: GGACCCGGGTCC, GGA4mCCCGGGTCC, GGA5mCCCGGGTCC, CGCGCGCG, CG4mCGCGCG, CG5mCGCGCG were synthetized to study the contribution of methyl groups into the energetics of the three known cooperative transitions in DNA: helix-coil, B-A and B-Z With the use of circular dichroism and absorbtion methods the profiles of the above transitions were obtained by variation of temperature (helix-coil), trifluoroethanol fraction (B-A), NaCl and trifluorethanol contents (B-Z). On the basis of the transition widths and shifts of the transition points due to the methylations the energetics of the methyl groups was estimated. 5mC stabilizes the B form relatively the A form by 0.
View Article and Find Full Text PDFThe synthesis of N4-methyl-2'-deoxycytidine and its fully protected mononucleotide, suitable for the oligonucleotide synthesis by phosphotriester method is described. A set of octanucleotides - d(CGCGCGCG), d(CG5mCGCGCG), d(CG4mCGCGCG) and dodecanucleotides - d(GGACCCGGGTCC), d(GGA5mCCCGGGTCC), d(GGA4mCCCGGGTCC) has been synthesized in a solution. Physical characterization of the oligonucleotide duplexes by means of UV and CD spectrometry provides the evidence that 4mC similarly to 5mC favours the B--greater than Z transition, although both of these methylated cytosines inhibit the B--greater than A conformational change.
View Article and Find Full Text PDFJ Biomol Struct Dyn
December 1986
Self-complementary decadeoxynucleotides, CCGATATCGG, CCAGATCTGG, CCCTGCAGGG, GGGGGCCCCC, were designed and synthesized to estimate the A-philic free energy of CC/GG contacts. First, regions of temperature-stability of the double-stranded conformation were determined for each 10-mer. Then, circular dichroism spectra were recorded for the B-family forms at different temperatures, counter-ion concentrations and trifluoroethanol contents.
View Article and Find Full Text PDFThe Interaction of the cro protein of lambda phage with a synthetic OR3 operator having 17 base pairs in length and with its 9 bp fragment has been studied using the circular dichroism (CD) method. In both cases, a considerable change in the CD of the samples was found in the region 260-300 nm upon the addition of the cro protein. The stoichiometry obtained by the CD titration was identical for OR3 and its 9 bp fragment: one duplex per dimeric cro.
View Article and Find Full Text PDFConformations of the synthetic deoxyoligonucleotide 17 base pairs long, which is an OR3 operator of lambda phage, and of its 9-b.p. fragment were studied by the circular dichroism method (CD).
View Article and Find Full Text PDFThe B-A transition is characterized by two main physical parameters which might be biologically important: the cooperativity length and free energy difference between the B and A states under physiological conditions. Earlier these values were determined by us in an experiment over the B-A shift in water-non-electrolyte solutions in the presence of small molecules ("ties") affecting the B-A equilibrium. Now we report a new method of determining the cooperativity length which utilizes a phase diagram (B,A, coil).
View Article and Find Full Text PDFRelative accessibility of nucleosomal histones to acetic anhydride during acetylation has been studied as a function of concentration, pH and ionic strength of the solution using high-resolution gel-electrophoresis. It was shown that about 80% of lysine residues in nucleosomal histones and 100% of the same residues in histone complexes without DNA in 2 M NaCl are accessible to the modification, which is proved by the localization of the majority of lysine residues in nucleosomes near the surface of the histone octamer, by their participation in ionic interactions with DNA and, probably, in histone-histone contacts. Gel-electrophoretic experiments with nucleosomes and studies of the histone resistance to mild trypsinolysis indicated that neither nucleosomes themselves nor histone octamers are affected even though 50% of lysine residues in histones have been acetylated.
View Article and Find Full Text PDFCold Spring Harb Symp Quant Biol
August 1983
Biochim Biophys Acta
September 1979
The complexex DNA-Ag1+, DNA-Cu1+, protonated DNA and DNA methylated at N7 of guanine were oriented by pumping the solutions through a multicapillary cell in the direction of a light beam. The CD components along the DNA axis, delta epsilon parallel, and normal to it, 2 delta epsilon perpendicular, were calculated from the CD spectra of the oriented samples by the method of Chung and Holzwarth, (1975) J. Mol.
View Article and Find Full Text PDFThe degree of orientation of DNA in a flow has been studied within the interval of the B - A transition induced by ethanol. The orientation of the B DNA (60-65% ethanol, v/v) and that of the A DNA (80-82% ethanol) are nearly identical. This means that both conformations have similar persistence lengths and that there is no aggregation in the course of formation of the A form.
View Article and Find Full Text PDFThe native T2 DNA in solutions with different LiCl concentrations was oriented by pumping through a capillary device similar to that described in rf. 1. The change of the parallel, deltaepsilon parallel, and perpendicular, 2 delta epsilon perpendicular, components of circular dichroism tensor was studied as a function of salt concentration.
View Article and Find Full Text PDFThe circular dichroism (CD) spectra of flow-oriented complexes of DNA with proflavine (PF), ethidium (ET) and distamycine (DS) have been studied in the ultraviolet region. The CD spectra with light propagating in parallel to the flow direction were measured by the method of Chung and Holzwarth [1]. Delta epsilon and delta epsilon values have been obtained by this method.
View Article and Find Full Text PDFThe binding of ethidium bromide and acriflavin dyes with DNA modified with a spin-labelled analogue of ethylene imine has been studied. These spin-labels were shown to bind covalently to DNA, at the same time the number of the dye molecules bound is decreased without any changes in the binding constant. Analysis of ESR spectra of the samples in the frozen 50% water-glycerol solution at 77 degrees K for spin-labelled DNA has shown that addition of the dyes increases distance between the labels.
View Article and Find Full Text PDFCircular dichroic spectra of A-DNA in 78% ethanol and of tRNA in water and ethanol solutions have been studied at different concentrations of NaCl. An increase in the Na+ concentration from 0.5.
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