Cross-linked polyacrylamide gel electrophoresis of single-stranded DNA for microfabricated genomic analysis systems

Microfabricated devices are poised to offer inexpensive self-contained alternatives to conventional benchtop-scale laboratory equipment for performing a variety of important DNA analysis assays. In order to realize the dramatic cost savings possible through photolithographic fabrication techniques, these devices must occupy an extremely compact footprint on the silicon wafer. This requirement implies that electrophoretic separations must be performed over ultrashort distances. Employing cross-linked polyacrylamide gels in place of conventional uncross-linked sieving media offers a convenient strategy to achieve this goal. In this paper, we show how the increased resolving power offered by cross-linked polyacrylamide gels, along with improved sample injection techniques, can be exploited to enhance separation performance in microscale systems. We use these techniques to perform high-resolution gel electrophoresis of single-stranded DNA fragments in microfabricated devices over separation distances of 1.5 cm or less. The results presented here are in agreement with theoretical predictions and suggest that it is possible to perform DNA sequencing on compact microchips. More importantly, the separation performance demonstrated in this work is already more than adequate to perform a number of important genomic assays imposing less stringent resolution requirements than sequencing. Successfully adapting even a few of these assays to the microdevice format has the potential to provide a new generation of inexpensive and portable devices suitable for direct end-user applications.     

Purification of genomic DNA by short monolithic columns

The isolation and purification of nucleic acids is essential for many procedures in molecular biology. After showing that bacterial and eukaryotic genomic DNA can be specifically bound to the CIM DEAE monolithic column, this characteristic was exploited in development of a simple and fast chromatographic procedure for isolation and purification of genomic DNA from cell lysates that does not include the usage of toxic organic solutions. The purity and the quality of the isolate as well as the duration of the procedure was similar to other chromatographic methods used today for isolation of genomic DNA, but the initial sample volume was not restricted.     

Rapid determination of genomic DNA length for new bacteriophages

dsDNA viruses with long genomes (>200 kb) are expected to be a major source of novel genes. To rapidly characterize the genomes of newly isolated dsDNA bacteriophages, we develop here a procedure for the PFGE of intact long DNA genomes from bacteriophage particles in unfractionated, infected cell lysates of either liquid or gelled cultures. The DNA used for PFGE is suitable for sequencing after extraction with phenol. The PFGE is tuned to the range of expected DNA lengths. This procedure bypasses the isolation of bacteriophage particles and is useful for PFGE analysis of DNA from dissected zones of bacteriophage plaques.     

Capillary electrophoresis-laser induced fluorescence analysis of endogenous damage in mitochondrial and genomic DNA

Reactive oxygen molecules are formed in vivo as by-products of normal aerobic metabolism. All organisms dependent on oxygen are inevitably exposed to these species so that DNA damage can occur in both genomic and mitochondrial DNA (mtDNA). In order to determine endogenous DNA damage we have developed an analytical method that involves the isolation and hydrolysis of genomic DNA or mtDNA, the labeling of modified and unmodified nucleotides and micellar electrokinetic chromatography with laser-induced fluorescence detection. With this method we have found etheno-adenine, thymine glycol, uracil, hypoxanthine, and 5-methylcytosine. These were identified by the addition of internal standards to the genomic or mtDNA. There are a large number of other signals in the electropherograms of mtDNA that we have never found in genomic DNA analysis because they are at lower concentration in the genome. In the DNA of untreated patients with chronic lymphocytic leukemia (CLL), uracil and high levels of etheno-adenine were found, which can be explained by antioxidant enzyme alterations and oxidative stress in the CLL lymphocytes.     

Magnetic hydrophilic methacrylate-based polymer microspheres for genomic DNA isolation

Carboxyl groups containing magnetic and non-magnetic microspheres were used in solid-phase reversible immobilization (SPRI) of genomic DNA. Magnetic non-porous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate)--P(HEMA-co-EDMA), poly(glycidyl methacrylate)--PGMA and P(HEMA-co-GMA) microspheres with hydrophilic properties were prepared by dispersion copolymerization of the respective monomers in the presence of colloidal iron oxides. DNA from chicken erythrocytes and DNA isolated from bacterial cells of Bifidobacterium longum was used for testing of adsorption/desorption properties of magnetic microspheres. The occurrence of false negative results in polymerase chain reaction (PCR) caused by the presence of extracellular inhibitors in DNA samples has been solved using SPRI. The P(HEMA-co-EDMA) and P(HEMA-co-GMA) microspheres were used for isolation of DNA from different dairy products followed by PCR identification of Bifidobacterium strains.     

High speed analysis in packed columns. Part II. Some guidelines and procedures for time optimisation

Summary The work described in Part I has been extended to show that the basic equation derived therein can be reduced to allow a direct analytical solution. For convenience, solution by this technique is termed DAMAT-X (Direct Approach Minimising Analysis time based on X) to distinguish it from solutions obtained by the technique in Part I, named here simply DAMAT. An additional advantage of the reduced equation is that some solutions are readily available by inspection and this feature is illustrated diagrammatically. Finally it is indicated how DAMAT-X can be used as the basis for assessing the accuracy of other techniques based on the (h/ū) group, but which require less data for approximating to minimising conditions.     

A new ion-exchange adsorbent with paramagnetic properties for the separation of genomic DNA

A new ion-exchange adsorbent (IEA) derived from Fe(3)O(4)/SiO(2)-GPTMS-DEAE with paramagnetic properties was prepared. Fe(3)O(4) nanoparticles were firstly prepared in water-in-oil microemulsion. The magnetic Fe(3)O(4) particles were modified in situ by hydrolysis and condensation reactions with tetraethoxysilane (TEOS) to form the core-shell Fe(3)O(4)/SiO(2). The modified particles were further treated by 3-glycidoxypropyltrimethoxysilane (GPTMS) to form Fe(3)O(4)/SiO(2)-GPTMS nanoparticles. Fe(3)O(4)/SiO(2)-GPTMS-DEAE nanoparticles (IEA) were finally obtained through the condensation reaction between the Cl of diethylaminoethyl chloride-HCl (DEAE) and the epoxy groups of GPTMS in the Fe(3)O(4)/SiO(2)-GPTMS. The obtained IEA has features of paramagnetic and ion exchange properties because of the Fe(3)O(4) nanoparticles and protonated organic amine in the sample. The intermediates and final product obtained in the synthesis process were characterized. The separation result of genomic DNA from blood indicated that Fe(3)O(4)/SiO(2)-GPTMS-DEAE nanoparticles have outstanding advantages in operation, selectivity, and capacity.     

Characterizations for Some Types of DNA Graphs

Vertex induced subgraphs of directed de Bruijn graphs with labels of fixed length k and over α letter alphabet are (α,k)-labelled. DNA graphs are (4,k)-labelled graphs. Pendavingh et al. proved that it is NP-hard to determine the smallest value α _k (D) for which a directed graph D can be (α _k (D),k)-labelled for any fixed . In this paper, we obtain the following formulas: and for cycle C _n and path P _n . Accordingly, we show that both cycles and paths are DNA graphs. Next we prove that rooted trees and self-adjoint digraphs admit a (Δ,k)-labelling for some positive integer k and they are DNA graphs if and only if Δ ≤ 4, where Δ is the maximum number in all out-degrees and in-degrees of such digraphs.     

Label-free colorimetric detection of specific sequences in genomic DNA amplified by the polymerase chain reaction

We document the surprising result that single-stranded DNA adsorbs on negatively charged gold nanoparticles (Au-nps) with a rate that depends on sequence length and temperature. After ss-DNA adsorbs on Au-nps, we find that the particles are stabilized against salt-induced aggregation. These observations can be rationalized on the basis of electrostatics and form the basis for a colorimetric assay to identify specific sequences and single nucleotide polymorphisms on polymerase chain reaction (PCR)-amplified DNA. The assay is label-free, requires no covalent modification of the DNA or Au-np surfaces, and takes on the sensitivity of PCR. Most important, binding of target and probe takes place in solution where hybridization occurs in less than 1 min. As an example, we test PCR-amplified genomic DNA from clinical samples for single nucleotide polymorphisms (SNPs) associated with a fatal arrhythmia known as long QT syndrome.     

Detection of fragmented genomic DNA by PCR-free piezoelectric sensing using a denaturation approach

Label-free and real-time DNA sequence detection in PCR-amplified DNA samples can now be achieved by different approaches. On the contrary, only few works have been reported dealing with direct sequence detection in nonamplified genomic DNA. Here, a piezoelectric biosensor for direct detection of sequences in nonamplified genomic DNA is described. The system relies on real-time and label-free detection of the hybridization reaction between an immobilized probe and the complementary sequence in solution. The DNA probe is immobilized on the sensing surface (10 MHz quartz crystals), while the complementary sequence is present in the genomic DNA, previously fragmented with restriction enzymes.     

CLP-type data validation guidelines for neutron activation analysis

Neutron activation analysis data quality must be validated to serve evidentiary purposes for environmental restoration and health protection projects. This paper gives a basis for determining the technical validity of neutron activation analysis data.     

Evaluation of plasmid and genomic DNA calibrants used for the quantification of genetically modified organisms

The reliable quantification of genetically modified organisms (GMOs) by real-time PCR requires, besides thoroughly validated quantitative detection methods, sustainable calibration systems. The latter establishes the anchor points for the measured value and the measurement unit, respectively. In this paper, the suitability of two types of DNA calibrants, i.e. plasmid DNA and genomic DNA extracted from plant leaves, for the certification of the GMO content in reference materials as copy number ratio between two targeted DNA sequences was investigated. The PCR efficiencies and coefficients of determination of the calibration curves as well as the measured copy number ratios for three powder certified reference materials (CRMs), namely ERM-BF415e (NK603 maize), ERM-BF425c (356043 soya), and ERM-BF427c (98140 maize), originally certified for their mass fraction of GMO, were compared for both types of calibrants. In all three systems investigated, the PCR efficiencies of plasmid DNA were slightly closer to the PCR efficiencies observed for the genomic DNA extracted from seed powders rather than those of the genomic DNA extracted from leaves. Although the mean DNA copy number ratios for each CRM overlapped within their uncertainties, the DNA copy number ratios were significantly different using the two types of calibrants. Based on these observations, both plasmid and leaf genomic DNA calibrants would be technically suitable as anchor points for the calibration of the real-time PCR methods applied in this study. However, the most suitable approach to establish a sustainable traceability chain is to fix a reference system based on plasmid DNA.     

Multiple-channel microchips for high-throughput DNA analysis by capillary electrophoresis

Capillary electrophoresis on microfabricated multiple-channel chips has great potential for high-throughput analysis. This review focuses on multiple-channel chips used for high-throughput DNA analysis. It covers progress in the design and fabrication of multiple-channel chips and detection schemes used on these chips. Applications are concentrated on DNA fragment sizing, genotyping, and sequencing.     

Direct detection of genomic DNA by enzymatically amplified SPR imaging measurements of RNA microarrays

A novel surface enzymatic reaction scheme that amplifies the optical response of RNA microarrays to the binding of complementary DNA is developed for the direct detection and analysis of genomic DNA. The enzyme RNase H is shown to selectively and repeatedly destroy RNA from DNA-RNA heteroduplexes on gold surfaces; when used in conjunction with the label-free technique of surface plasmon resonance (SPR) imaging, DNA oligonucleotides can be detected at a concentration of 1 fM. This enzymatically amplified SPR imaging methodology is then utilized to detect and identify the presence of the TSPY gene in human genomic DNA without PCR amplification.     

Control of the compaction/unfolding transition of genomic DNA by the addition/disruption of lipid assemblies

We studied the interaction between individual long genomic DNA molecules and cationic lipid assemblies. The assembly of cationic lipid molecules into small unilamellar vesicles (SUVs) of about 50 nm diameter led to the compaction of DNA whereas the addition of a neutral surfactant resulted in the disruption of SUVs and the unfolding of DNA. This reversible process does not require any chemical reaction or change in the ionic strength of the solution. It was applied to switch DNA repeatedly between a compact and an unfolded conformation in a dynamic manner.     

PNA-based reagents for the direct and site-specific synthesis of thymine dimer lesions in genomic DNA

An acetophenone containing PNA-based reagent was designed for the direct and site-specific synthesis of a cis-syn thymidine dimer lesion in genomic DNA.     

DNA molecule manipulation by motor proteins for analysis at the single-molecule level

Massively parallel and individual DNA manipulation for analysis has been demonstrated by designing a fully self-assembled molecular system using motor proteins. DNA molecules were immobilized by trapping in a polyacrylamide gel replica, and were digested by a restriction enzyme, XhoI, for DNA analysis. One end of the λDNA was modified with biotin and the other end was modified with digoxin molecules by fragment labeling and ligation methods. The digoxin-functionalized end was immobilized on a glass surface coated with anti-digoxigenin antibody. The biotinylated end was freely suspended and experienced Brownian motion in a buffer solution. The free end was attached to a biotinylated microtubule via avidin–biotin biding and the DNA was stretched by a kinesin-based gliding assay. A stretched DNA molecule was fixed between the gel and coverslip to observe the cleavage of the DNA by the enzyme, which was supplied through the gel network structure. This simple process flow from DNA manipulation to analysis offers a new method of performing molecular surgery at the single-molecule scale. Figure DNA molecule manipulation by motor proteins for analysis at the single-molecule level