Denaturation of covalently closed circular DNA. Kinetics, comparison of several DNAs, mechanism and ionic effects

Fast separation of DNA sequencing fragments in highly alkaline solutions of linear polyacrylamide using electrophoresis in bare silica capillaries

An optimized procedure for the fast separation of DNA sequencing fragments in short bare fused-silica capillaries filled with highly alkaline solutions of replaceable linear polyacrylamide is presented. High denaturing abilities of the separation media at pH values over 12 are the main reason for their applications in analyses of ssDNA fragments. Moreover, the alkaline solutions of polyacrylamide provide other advantageous properties: three times higher electrophoretic mobility of ssDNA fragments in comparison to those in urea, negligibly low electroosmotic flow in uncoated capillaries, and an adequate stability to a fast alkaline hydrolysis. The separation power of this procedure is enhanced strongly by using monocarboxy poly(ethylene glycol), a terminator for transient isotachophoresis, which eliminates the electromigration dispersion. A high separation efficiency of our system enables to reduce analysis time to several minutes by decreasing the effective lengths of capillaries to 7 cm. A special sample introduction by diffusion is successfully applied. The experimental results demonstrate a potential of the alkaline electrolytes for an implementation in diagnostic sequencing practice.

Highly alkaline electrolyte for single-stranded DNA separations by electrophoresis in bare silica capillaries

A new, highly denaturing electrolyte system based on a solution containing 0.01 M NaOH, 0.0015 M Na2B4O5(OH)4 and a replaceable polymer sieving medium was designed for the separation of single-stranded DNA fragments in bare fused-silica capillaries. Extreme denaturing power, together with the optimized composition of the electrolyte, allows for a separation efficiency as high as 2,300,000 height equivalents to a theoretical plate per meter. Sample denaturation in alkaline solutions provides single-stranded DNA fragments without any intra- or intermolecular interactions at room temperature. Their electrophoretic mobilities were found to be twice those of fragments denatured by dimethylformamide or HCl. This can be interpreted in terms of an increased effective charge on the DNA molecules. The surprisingly weak electroosmosis (6 x 10(-10) m2 V-1 s-1) of polymer solutions at pH 12 or higher is considered to be the result of the dissolution of the silica capillary wall. A highly viscous thin layer of dissolved silica probably causes a shift of the slipping plane further away from the wall to the lower value of the zeta potential. Applications of the electrolyte in clinical diagnostics demonstrate its remarkable properties.

Cyclic voltammetry of submicrogram quantities of supercoiled, linear and denatured DNAs with DNA-modified mercury electrode

We have previously shown that a DNA-modified electrode can be prepared by immersing the hanging mercury drop electrode (HMDE) in a small volume (about 5-10 microliters) of a DNA solution. Within a short period of time the DNA is irreversibly adsorbed at the electrode, resisting subsequent washing. The electrode is then transferred into a voltammetric cell filled with the background electrolyte (that does not contain any nucleic acid) in which the voltammetric measurements are performed. This procedure is called adsorptive transfer stripping voltammetry (AdTSV). In this paper AdTS cyclic voltammetry (CV) peaks of DNA were measured to report on the stability of the attachment of plasmid DNA molecules to the electrode surface. It was shown that the attachment of plasmid DNA to the electrode was, like the case of calf thymus DNA, sufficiently stable. If the DNA-modified electrode was immersed in a protein solution no significant exchange between the DNA and protein was observed. Submicrogram amounts of DNA were sufficient to attain full coverage of the electrode at relatively short waiting times and the detection limit of the denatured DNA was below 2 ng. The intensity of the AdTS CV signals of supercoiled, linearized and thermally denatured linear DNAs differed from one another. It was shown that alkaline denaturation of linear and supercoiled DNA in solution can be studied using AdTS CV technique. It was further shown that at neutral pH the linearized plasmid undergoes denaturation due to a prolonged contact with the electrode charged to potentials around -1.2 V. Such a surface denaturation has been previously observed with calf thymus DNA and synthetic double-stranded polynucleotides. Our results show that in contrast to linear DNA, supercoiled DNA was not significantly denatured as a result of its prolonged contact with the electrode charged to various potentials in the range between -0.1 to -1.5 V.

Sequence-specific chemical modification of double-stranded DNA with alkylating oligodeoxyribonucleotide derivatives

Chemical modification of double-stranded (ds) DNA with alkylating oligodeoxynucleotide (oligo) derivatives, 5'-p(N-2-chloroethyl-N-methylamino) benzylamides of oligos, has been investigated. In contrast to relaxed plasmid DNAs, the superhelical molecules interact with the oligo derivatives and specific alkylation of the DNAs occurs at the regions complementary to the oligo reagents. Alkylating derivatives of oligocytidylates and pT(pCpT)6 react with corresponding homopyrimidine-homopurine tracts within ds DNA fragments due to triple helix formation.