Fast, sensitive point of care electrochemical molecular system for point mutation and select agent detection.

Point of care molecular diagnostics benefits from a portable battery-operated device capable of performing a fast turnaround using reliable inexpensive cartridges. We describe a prototype device for performing a molecular diagnostics test for clinical and biodefense samples in 16 minutes using a prototype capable of an 8 minute PCR reaction, followed by hybridization and detection on an electrochemical microarray based on the i-STAT® system. We used human buccal swabs for hemochromatosis testing including in-device DNA extraction. Additional clinical and biodefense samples included influenza A and bacterial select agents Bacillus anthracis, Yersinia pestis and Francisella tularensis.

Mutation identification DNA analysis system (MIDAS) for detection of known mutations.

We introduce a novel experimental strategy for DNA mutation detection named the Mismatch Identification DNA Analysis System (MIDAS) [1, 2], which has an associated isothermal probe amplification step to increase target DNA detection sensitivity to attomole levels. MIDAS exploits DNA glycosylases to remove the sugar moiety on one strand (the probe strand) at a DNA base pair mismatch. The resulting apyrimidinic/ apurinic (AP) site is cleaved by AP endonucleases/lyases either associated with the DNA glycosylase or externally added to the reaction mixture. MIDAS utilizes 32p- or FITC-labeled oligonucleotides as mutation probes. Generally between 20-50 nucleotides in length, the probe hybridizes to the target sequence at the reaction temperature. Mismatch repair enzymes (MREs) then cut the probe at the point of mismatch. Once the probe is cleaved, the fragments become thermally unstable and fall off the target, thereby allowing another full-length probe to hybridize. This oscillating process amplifies the signal (cleaved probe). Cleavage products can be detected by electrophoretic separation followed by autoradiography, or by laser-induced fluorescence-capillary electrophoresis (LIF-CE) of fluorophore-labeled probes in two minutes using a novel CE matrix. In the present experiments, we employed the mesophilic Escherichia coli enzyme deoxyinosine 3'-endonuclease (Endo V), and a novel thermostable T/G DNA glycosylase, TDG mismatch repair enzyme (TDG-MRE). MIDAS differentiated between a clinical sample BRCA 1 wild-type sequence and a BRCA1 185delAG mutation without the need for polymerase chain reaction (PCR). The combination of MIDAS with LIF-CE should make detection of known point mutations, deletions, and insertions a rapid and cost-effective technique well suited for automation.

The use of dynamic size-sieving capillary electrophoresis and mismatch repair enzymes for mutant DNA analysis.

The detection of base pair mismatches in limiting amounts of DNA is important in the early diagnosis of cancer and other genetic diseases. The specific type and exact location of a bp mismatch in certain genes can yield information on the likelihood of a patient developing a genetic disease, as well as the severity of the disease. We demonstrate two methods of specific DNA point mutation detection and identification that involve the integration of mismatch repair cleavage enzyme analyses with dynamic size-sieving capillary electrophoresis. The mismatch repair cleavage enzymes employ the very mechanism that a cell uses in its own mismatch recognition and repair systems. One analysis employs an isothermal signal amplification process, and the other involves polymerase chain reaction (PCR) (Hoffmann-LaRoche, Nutley, NJ, U.S.A.) for amplification of the DNA. Separation of the DNA fragments using dynamic size-sieving CE yields a cleaved fragment, providing definitive evidence of a bp mismatch. The specificity and sensitivity of the assay are facilitated by the detection of fluorescently labeled DNA fragments using laser-induced fluorescence detection; picogram quantities of a target DNA can be analyzed reproducibly.

Analysis of DNA fragmentation using a dynamic size-sieving polymer solution in capillary electrophoresis.

Various natural and induced processes cause DNA fragmentation. Examples of these processes include apoptosis, enzymatic digestion, free radical production from ionizing radiation, photoscission by laser radiation and thermal degradation. Slab gel electrophoresis has been used most often to monitor such DNA damage. We have investigated with capillary electrophoresis the use of a new size-sieving polymer solution, TreviSol-CE (TS-CE), to monitor the DNA fragments produced from a variety of degradation processes. This polymer solution provides high run-to-run migration time and peak width reproducibilities and high separation efficiency of double-stranded DNA fragments in the 500 to 7000 base pair size range. Analysis of apoptotic DNA fragments suggested the presence of multiple nucleosomes within each cell type investigated. For irradiated DNA standards, peak-width-at-half-height and peak area were used to monitor the progress of DNA fragmentation. For both apoptotic DNA and irradiated DNA standards, fine structural features of fragmentation were revealed.

The characterization of a new size-sieving polymeric matrix for the separation of DNA fragments using capillary electrophoresis.

A low-viscosity, polysaccharide matrix (TreviSol-CE [TS-CE], Trevigen, Inc., Gaithersburg, MD, U.S.A.) has been characterized experimentally in capillary electrophoresis for the separation of DNA fragments. The mass fraction (%) of the matrix in buffer solution and the applied field strength may be varied according to the size of DNA fragments to be separated. The use of tris-phosphate-EDTA (TPE) buffer at pH 7, instead of the more commonly used tris-borate-EDTA (TBE) and tris-acetate-EDTA (TAE) buffers at pH 8.3, provides higher separation efficiency in conjunction with this matrix and simultaneously preserves the internal coating of the capillary for high run-to-run reproducibility. In comparison with other commercially available DNA separation matrices for CE, TS-CE provides enhanced separation ability of DNA fragments greater than 600 base pairs (bp) in length and lower UV absorbance background for enhanced detectability.

The use of a new gel matrix for the separation of DNA fragments: a comparison study between slab gel electrophoresis and capillary electrophoresis.

TreviGel-500, a new polysaccharide matrix containing AgaCryl, commercially available as a powder for slab gel electrophoresis, is now being applied to the separation of DNA fragments in capillary electrophoresis. The capillary mode allows the use of one to two orders of magnitude lower mass fractions of matrix and approximately five to six orders of magnitude lower sample quantities than the slab gel electrophoresis counterpart for optimal separation of DNA fragments in the 100 to 2,000 base pair size range. In the capillary mode, this new separation matrix forms a semi-rigid gel that demonstrates enhanced selectivity for DNA fragments in the 1,000 to 7,000 base pair size range relative to alternative size-sieving polymer solutions. In addition, this matrix offers the advantages of lower toxicity than acrylamide. Comparisons are drawn between the use of this matrix in both slab gel electrophoresis and capillary electrophoresis for the separation of DNA fragments with respect to the mass fraction of the matrix in buffer, the buffer composition and sample loading or injection parameters.

Alternative to polyacrylamide gels improves the electrophoretic mobility shift assay.

In this paper we outline a simplified protocol for the electrophoretic mobility shift assay utilizing TreviGel 500, a nontoxic alternative to polyacrylamide. The TreviGel 500 matrix combines the strength and resolution of polyacrylamide with the simplicity and flexibility of agarose in the casting of gels. Therefore, this method provides a simple, rapid and nontoxic alternative to current protocols for the investigation of protein: DNA interactions.

A novel Tn10 tetracycline regulon system controlling expression of the bacteriophage T3 gene encoding S-adenosyl-L-methionine hydrolase.

To study the effects of in vivo DNA methylation, we have developed an inducible system to control the intracellular concentration of S-adenosyl-L-methionine (AdoMet). The product of the bacteriophage T3 AdoMet hydrolase-encoding gene (amh), which degrades AdoMet to L-homoserine and 5'-methylthioadenosine, was employed to lower AdoMet concentrations in vivo. The amh gene was placed downstream from the inducible tetA promoter of the Tn10 tetracycline regulon substituting for most of the tetA gene. Unlike in the original isolates [Hughes et al., J. Bacteriol. 169 (1987) 3625-2632], this promoter allows controlled expression. These constructs are stable and can be induced in a dose-dependent manner. The system is maximally induced 2-3 h after addition of the inducer, autoclaved chlortetracycline (cTc). DNA methylation in vivo was assessed in this model system by BamHI cleavage of plasmid DNA isolated from cells cotransformed by two compatible plasmids, one carrying the inducible amh gene, the other M.BamHII methyltransferase encoding gene. The induction of amh decreased the intracellular pool of AdoMet which M.BamHII requires as a cofactor. Under these conditions, there is a decrease in DNA methylation. The unmethylated DNA is assayed by BamHI cleavage. This system will be useful for studying transcription, DNA replication, gene repair and other cellular phenomena affected by methylation.

Expression of dopamine beta-hydroxylase in Drosophila Schneider 2 cells. Evidence for a mechanism of membrane binding other than uncleaved signal peptide.

To characterize the mechanism of membrane attachment of dopamine beta-hydroxylase, an expression system producing the processed form of this enzyme has been developed. We have replaced the endogenous signal peptide of bovine dopamine beta-hydroxylase with a heterologous signal peptide which is efficiently recognized and cleaved in Drosophila Schneider 2 cells. A cDNA encoding this chimeric recombinant bovine enzyme has been stably transfected into Schneider 2 cells. The inducible expression of active dopamine beta-hydroxylase in these cells has been verified by Western blotting and enzyme activity assays. N-terminal sequence analysis of purified recombinant enzyme demonstrates complete removal of the signal peptide. Subcellular analysis shows that the recombinant enzyme exists as both a soluble and a membrane-bound form in these cells. These data demonstrate that the endogenous signal peptide is not required for the formation of the membranous dopamine beta-hydroxylase and further that the enzyme can be bound to membranes via a mechanism other than uncleaved signal sequence.