Development of salt-tolerance interface for an high performance liquid chromatography/inductively coupled plasma mass spectrometry system and its application to accurate quantification of DNA samples.

Accurate quantification of DNA is highly important in various fields. Determination of phosphorus by ICP-MS is one of the most effective methods for accurate quantification of DNA due to the fixed stoichiometry of phosphate to this molecule. In this paper, a smart and reliable method for accurate quantification of DNA fragments and oligodeoxythymidilic acids by hyphenated HPLC/ICP-MS equipped with a highly efficient interface device is presented. The interface was constructed of a home-made capillary-attached micronebulizer and temperature-controllable cyclonic spray chamber (IsoMist). As a separation column for DNA samples, home-made methacrylate-based weak anion-exchange monolith was employed. Some parameters, which include composition of mobile phase, gradient program, inner and outer diameters of capillary, temperature of spray chamber etc., were optimized to find the best performance for separation and accurate quantification of DNA samples. The proposed system could achieve many advantages, such as total consumption for small amount sample analysis, salt-tolerance for hyphenated analysis, high accuracy and precision for quantitative analysis. Using this proposed system, the samples of 20 bp DNA ladder (20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 300, 400, 500 base pairs) and oligodeoxythymidilic acids (dT(12-18)) were rapidly separated and accurately quantified.

[Determination of the cysteine residues in the surface-confined biomolecules by using electrochemical desorption and fluorescence detection].

To develop a method for the detection of surface-confined peptides containing cysteine residues or oligodeoxynucleotides (ODNs) whose 3' ends modified with thiol groups, and a thiol-specific fluorescent cross-linker, N-(9-acridinyl) maleimide (NAM) was used. The peptides studied herein include both the oxidized and reduced forms of glutathione, and a hexapeptide (FT). Peptides are first attached onto the activated 11-mercaptoundecanoic acid (MUA)-terminated alkanethiol self-assembled monolayers (SAMs) and then derivatized with NAM. The cysteine residues was determined by using electrochemical desorption and fluorescence detection. GSH concentration as low as 40 pmol x L(-1) can be measured. The fluorescence intensity in the case of FT is about 3 times as high as that for GSH, which is consistent with the molar ratio of cysteine residues in these two molecules. The analytical performance of gene analysis was also evaluated through the analyses of a complementary target and targets with varying numbers of mismatching bases. The method described here is simple, sensitive, reproducible, and does not require sophisticated analytical instrumentation and separation procedures.

[Establishment, optimization and application of a screening method for immunoregulatory oligodeoxynucleotides].

AIM: To establish a set of reasonable and convenient experimental system to provide a screening method for the development of novel immunoregulatory oligodeoxynucleotides. METHODS: The human PBMCs were stimulated by CpG ODN and/or immunoregulatory ODN. The cell proliferation and anti-viral activity of the supernatant induced by CpG ODN were examined by thymidine incorporation and anti-viral bioassay to evaluate the immunoregulatory activity of candidate ODN. The experimental conditions were also optimized. RESULTS: A screening method on which A151, a positive immunoregulatory ODN, inhibited the proliferation and anti-viral activity of the CpG ODN-induced human PBMCs was successfully established. CONCLUSION: The successful establishment of CpG ODN based screening method lays the foundations for further development of novel immunoregulatory oligodeoxynucleotides.

Fabrication of microchambers defined by photopolymerized hydrogels and weirs within microfluidic systems: application to DNA hybridization.

This paper describes fabrication of serial microchamber arrays within the channels of a microfluidic device. The chambers are defined using a combination of weirs and UV-cross-linked hydrogel plugs (poly(ethylene glycol) diacrylates). This approach permits the microchambers to be addressed by pump-driven pressure in one dimension and by electrophoresis in the other. The function of the device is demonstrated by detecting DNA targets. Single-strand DNA (ssDNA) probes labeled with biotin were immobilized onto microbeads coated with streptavidin. The DNA-functionalized microbeads were packed into each of three microchambers by injection through inlet wells. Three oligonucleotides were designed as probes and four as targets. Hybridization reactions were performed by moving the targets across the array of probe-containing microchambers by electrophoresis. The hybridization of fluorescein-labeled ssDNA targets to complementary probes was observed by fluorescence microscopy. These studies resulted in four key observations: (1) there was no detectable binding of targets to noncomplementary probes; (2) hybridization was 90% complete within 1 min; (3) once captured, the targets could be independently released and recovered from the microbeads by treatment with 0.1 N NaOH; (4) multiple analyses could be performed using a single bead set, but there was degradation in performance after each capture/release cycle.

[Synthesis of oligodeoxyribothymidylate derivatives containing alkylating groups and residues of biotin, for directed modification of chromatin]. / Sintez proizvodnogo oligodezoksiribotimidilata, soderzhashchego alkiliruiushchuiu gruppu i ostatok biotina, dlia napravlennoi modifikatsii khromatina.

An oligodeoxythymidylate derivative bearing an alkylating group at the 5'-end and biotin at the 3'-end (RCl-(pdT)16-bio) was synthesized. This reagent alkylates polyA-tracts of DNA in HeLa nuclei specifically via complementary complexes with single-stranded segments of DNA and by the preliminary treatment of chromatin with S1-nuclease, since the reaction is inhibited by an excess of the corresponding free oligothymidylate. The reagent will be used to study the distribution of local unwinded parts of polyA-repeats of DNA in human chromatin by the electron microscopy.

Structure of the intrastrand cis-[Pt(NH3)2(d(GpCpG))] adduct in a dodecanucleotide duplex: I. A 1H and 31P n.m.r. study.

The structure of an intrastrand cis-[Pt(NH3)2(d(GpCpG))] adduct in a dodecanucleotide duplex has been investigated by using ultraviolet absorption, circular dichroism, 1H and 31P n.m.r. The binding of cis-DDP does not inhibit the formation of a duplex but it induces a lowering of congruent to 26 degrees C of its melting temperature. A broadening of the 1H spectrum prevents an accurate analysis of the platination site. Nevertheless, by considering its thermal behavior and the number of imino protons a model of structure of the platinated duplex is proposed in which the central C.G. pair is disrupted and a neighboring C.G pair is very accessible or distorted. The environment of two phosphate groups is disturbed by the cis-DDP binding.

Conformational analysis of hairpin oligodeoxyribonucleotides by a single-strand-specific nuclease.

Hairpin-forming oligodeoxynucleotides d[ATCCTA(A)NTAGGAT] with n = 3-6 were subjected to nuclease digestion with the nuclease from mung bean. Cleavage occurs only in the loop region of the hairpin molecules. In detail, the number and intensity of cleavage sites were determined in relation to the length of the loop, the temperature and the salt concentration. The restricted accessibility of mung bean nuclease to the loop bases adjacent to the helical region of all hairpins is due to a reduced exposure of these bases in presence of a certain Mg2+ concentration. With increasing temperature the exposure of these bases is increased. It is deduced that the bases adjacent to the helix increase the length of the latter by stacking, the degree of which is dependent on the number of loop bases.