A novel type of microscopic size chip based on double-stranded nucleic acids.

The double-stranded molecules of nucleic acids (NA) of B- and A-families fixed in the structure of cholesteric liquid-crystalline dispersions, formed as a result of phase exclusion of these molecules from polymer-containing solution, have been used as 'building blocks' for the molecular design. Using the formation of polymeric chelate bridges between NA molecules, three-dimensional structures consisting of alternating NA, anthracycline and copper ions, were created. The formation of the polymeric chelate bridges allows one to stabilize the initial spatial mode of ordering of neighboring NA molecules in a form of so-called 'molecular constructions', immobilize these constructions onto supporting film and evaluate their sizes and shape. The creation of NA molecular constructions is accompanied by an 'extra-increase' in the amplitude of the bands in the CD spectra, despite the initial sense of cholesteric twisting characteristic of liquid-crystalline dispersions. Destroying of polymeric chelate bridges between NA molecules by action of biologically relevant compounds results in disintegration of NA liquid-crystalline molecular constructions. Three-dimensional NA molecular construction can be used as a microscopic size multifunctional chemical unit (chip) for biological or chemical needs.

Novel Cholesteric Phase in Dispersions of Nucleic Acids due to Polymeric Chelate Bridges.

Physics, Moscow, RussiaWe consider cholesteric liquid-crystalline DNA dispersions, and show thatpolymeric (Dau-Cu) complexes, the so-called bridges, between pairs of DNA molecules may generate a super liquid-crystalline structure (BR-phase), charachterized by a soliton lattice of the spatial distribution of theorder parameter. The BR-phase could have a layered spatial structure andan abnormal optical activity that could have a bearing upon the intenseCD-band observed in DNA-dispersions.

Double-stranded nucleic acids in liquid-crystalline dispersions as building blocks for cross-linked supramolecular structures.

Double-stranded DNA fixed in a cholesteric liquid-crystalline dispersion was used for generating an ordered supramolecular structure in the presence of anthracycline and copper (II) ions. The structure is stable in a water-salt solution and does not require poly(ethyleneglycol).The ordered network can be immobilized on the surface of a polymeric film, and may collapse in the presence of biologically and pharmacologically relevant compounds. Accordingly, the DNA-based liquid-crystalline network represents the basis to obtain novel highly sensitive biosensing units.

Double-stranded DNA liquid-crystalline dispersions as biosensing units.

Three different approaches to constructing biosensing units based on double-stranded (ds) DNA molecules, capable of detecting various biologically active compounds, are considered. The first approach is based on the abnormal optical activity of the liquid-crystalline dispersion formed from ds DNA molecules, modified by relevant physical factors or treated with biologically active compounds. The second one is based on the abnormal optical activity of the liquid-crystalline dispersions formed first from the ds DNA and then treated with coloured biologically active compounds. The third one is based on the abnormal optical activity, specific to particles of the liquid-crystalline dispersions, where the neighbouring DNA molecules are crosslinked by artificial polymeric bridges. These approaches permit the detection of biologically relevant compounds of various origins.

Toroidal structures due to anisotropy of DNA-like molecules.

We suggest that toroidal structures in the state of psi-condensation of DNA may be caused by anisotropy on a meso-scale of several thousand A, the conformation of a DNA-molecule being determined by its elasticity and neutralization of phosphate charge. We model a molecule of B-DNA on an anisotropic elastic rod subject to a torque, and make the numerical simulation of the model that reveals that under appropriate conditions, which may be effected in experimental setting by changing the concentration of polymeric solutions, there are toroidal structures having the size of a few persistence lengths, in agreement with the experimental data. On changing the elastic modulii or characteristics of the counterion layer, we see the toroidal structures turn into the spherical ones. To understand the function of anisotropy it would be interesting to investigate the Z-DNA as regards psi-condensation.

Liquid-crystalline structure of nucleic acids: effect of antracycline drugs and copper ions.

The formation of liquid-crystalline dispersions (L.C.D.) from double-stranded DNA and polynucleotide (NA) molecules complexed with a number of anthracycline derivatives was investigated. These drugs form two types of complexes (complex I and complex II) with NA, which differ in the mode of drug orientation in respect to the NA helical axis. When complex II forms, addition of copper ions causes bridging of neighboring NA molecules through polymeric copper-anthracycline links (Figure 1). This results in an extra-increase in the amplitude of the intense CD band, characteristic for complex II, in the drug absorption region. Comparison of data obtained for different analogs and derivatives of daunomycin, has shown that the presence of 4 coordinating oxygen atoms at positions 5,6 and 11,12 (or 1,12) of the anthracycline ring system represents the basic prerequisite for the formation of a long polymeric chelate bridge after addition of copper ions. A second requirement relates to the chemical and stereochemical properties of sugar residues at position 7. These are important for proper positioning of the neighboring anthracycline aglycones in the polymeric chelate bridges and for spatial fixation of Cu2+ ions. Base sequence of double-stranded polynucleotides plays, if any, a minor role in polymeric chelate bridge formation. The question concerning the sterical orientation of two neighbouring antracyclines in the linking bridges, formed between NA molecules fixed in the liquid-crystalline structure, remains open.

Adjustable 'cross-linking' of neighboring DNA molecules in liquid-crystalline dispersions through (daunomycin-copper) polymeric chelate complexes.

The interaction of daunomycin molecules with double-stranded DNA in the liquid-crystalline state was investigated. It was shown that at a certain extent of daunomycin binding a change of the mechanism of anthracycline orientation with reference to the DNA chain occurs. This is testified by the alteration of the sense of spatial packing of the DNA molecules in liquid-crystalline dispersions formed as a result of phase separation in poly(ethyleneglycol)-containing solutions, as well as by the onset of the reaction of daunomycin with divalent copper ions. Using this reaction, polymeric (daunomycin-copper) chelate cross-links between the DNA molecules fixed in the liquid-crystalline dispersions were formed. The length of such cross-links as adjusted by the distance between the DNA molecules, which, in turn, depends on the concentration of poly(ethyleneglycol) used for phase separation. The above molecular building mechanism may lead to new interesting applications.

A new approach for creating double-stranded DNA biosensors.

The principle of 'sandwich'-type biosensors based on liquid-crystalline dispersions formed from [DNA-polycation] complexes is outlined. These biosensors will find application in the determination of a range of compounds and physical factors that affect the ability of a given polycationic molecule to maintain intermolecular crosslinks between neighbouring DNA molecules. In the case of liquid-crystalline dispersions formed from [DNA-protamine] complexes, the lowest concentration of hydrolytic enzyme (trypsin) detectable was approximately 10-(14) M.

The reduction of thymine residues in DNA by the combined action of UV light and hypophosphite.

UV irradiation (lambda = 254 nm) of thymine and uracil in aqueous solution containing salts of phosphinic acid (hypophosphites) results in the formation of the corresponding dihydropyrimidine derivatives. The peculiarities of this new photochemical reaction consist of a specificity towards 2,4-dioxophyrimidines, a high quantum yield and a neutral pH optimum. The quantum yield of photoconversion of thymine at pH 7.0 is equal to 1.9 x 10(-2) in 1 M NaH2PO2; it is diminished to 8.5 x 10(-3) in 0.1 M NaH2PO2. The same decrease in quantum yield with concentration is also found for uracil and uridine; quantum yields of their transformations in 0.1 M NaH2PO2 at pH 7.0 are 6.6 x 10(-2) and 1.5 x 10(-1) respectively. The mild conditions and high quantum yields characteristic of the photoinduced reaction above open up the possibility of obtaining DNA molecules which contain among pyrimidine photoproducts mainly dihydropyrimidine residues. A correlation between various types of thymine modifications in UV-irradiated double-stranded DNA (dimers and dihydrothymidine residues) and the amplitude of the intense negative band in the circular dichroism (CD) spectra specific for DNA liquid crystalline dispersions has been established. A possible application of this base-specific modification to the investigation of nucleic acids is considered.