Arthur Reis

Two-temperature LATE-PCR endpoint genotyping

BackgroundIn conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay.ResultsTwo-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE)-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA) and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of 2:1 and 1:2 ratios of the same alleles.ConclusionSNP genotyping via Two-Temperature LATE-PCR takes place in a homogeneous closed-tube format and uses a single hybridization probe per SNP site. These assays are convenient, rely on endpoint analysis, improve the options for construction of multiplex assays, and are suitable for SNP genotyping, mutation scanning, and detection of DNA duplication or deletions.

Fluorescent signatures for variable DNA sequences

Life abounds with genetic variations writ in sequences that are often only a few hundred nucleotides long. Rapid detection of these variations for identification of genetic diseases, pathogens and organisms has become the mainstay of molecular science and medicine. This report describes a new, highly informative closed-tube polymerase chain reaction (PCR) strategy for analysis of both known and unknown sequence variations. It combines efficient quantitative amplification of single-stranded DNA targets through LATE-PCR with sets of Lights-On/Lights-Off probes that hybridize to their target sequences over a broad temperature range. Contiguous pairs of Lights-On/Lights-Off probes of the same fluorescent color are used to scan hundreds of nucleotides for the presence of mutations. Sets of probes in different colors can be combined in the same tube to analyze even longer single-stranded targets. Each set of hybridized Lights-On/Lights-Off probes generates a composite fluorescent contour, which is mathematically converted to a sequence-specific fluorescent signature. The versatility and broad utility of this new technology is illustrated in this report by characterization of variant sequences in three different DNA targets: the rpoB gene of Mycobacterium tuberculosis, a sequence in the mitochondrial cytochrome C oxidase subunit 1 gene of nematodes and the V3 hypervariable region of the bacterial 16 s ribosomal RNA gene. We anticipate widespread use of these technologies for diagnostics, species identification and basic research.

Characterization of novel TCNQ and TCNE 1:1 and 1:2 salts of the tetrakis(dimethyamino)ethylene dication, [{(CH3)2N}2C–C{N(CH3)2}2]2+

Addition of TCNQ to a solution of tetrakis(dimethylamino)ethylene in MeCN produces the salt [TDAE][TCNQ]2; the dipositive cation, [{(CH3)2N}2C–C{N(CH3)2}2]2+, is nonplanar, with a dihedral angle of 63.9°, while the TCNQ anions crystallize as [TCNQ]22– dimers with an interplanar separation of 3.16 A. The complex [TDAE][TCNE] was prepared in a similar manner; the [TDAE]2+ cation and [TCNE]2– anion are nonplanar, with dihedral angles of 71.3 and 76.6°, respectively. The four CN groups in the [TCNE]2– anion each accept three C–H ⋯ N hydrogen bonds. In each case, one C–N ⋯ H angle is in the range 134–156°, while the other two are near 90°(81–100°).

Single-Molecule LATE-PCR Analysis of Human Mitochondrial Genomic Sequence Variations

It is thought that changes in mitochondrial DNA are associated with many degenerative diseases, including Alzheimers and diabetes. Much of the evidence, however, depends on correlating disease states with changing levels of heteroplasmy within populations of mitochondrial genomes, rather than individual mitochondrial genomes. Thus these measurements are likely to either overestimate the extent of heteroplasmy due to technical artifacts, or underestimate the actual level of heteroplasmy because only the most abundant changes are observable. In contrast, Single Molecule (SM) LATE-PCR analysis achieves efficient amplification of single-stranded amplicons from single target molecules. The product molecules, in turn, can be accurately sequenced using a convenient Dilute-‘N’-Go protocol, as shown here. Using these novel technologies we have rigorously analyzed levels of mitochondrial genome heteroplasmy found in single hair shafts of healthy adult individuals. Two of the single molecule sequences (7% of the samples) were found to contain mutations. Most of the mtDNA sequence changes, however, were due to the presence of laboratory contaminants. Amplification and sequencing errors did not result in mis-identification of mutations. We conclude that SM-LATE-PCR in combination with Dilute-‘N’-Go Sequencing are convenient technologies for detecting infrequent mutations in mitochondrial genomes, provided great care is taken to control and document contamination. We plan to use these technologies in the future to look for age, drug, and disease related mitochondrial genome changes in model systems and clinical samples.

Design and Construction of a Single-Tube, LATE-PCR, Multiplex Endpoint Assay with Lights-On/Lights-Off Probes for the Detection of Pathogens Associated with Sepsis

Aims. The goal of this study was to construct a single tube molecular diagnostic multiplex assay for the detection of microbial pathogens commonly associated with septicemia, using LATE-PCR and Lights-On/Lights-Off probe technology. Methods and Results. The assay described here identified pathogens associated with sepsis by amplification and analysis of the 16S ribosomal DNA gene sequence for bacteria and specific gene sequences for fungi. A sequence from an unidentified gene in Lactococcus lactis subsp. cremoris served as a positive control for assay function. LATE-PCR was used to generate single-stranded amplicons that were then analyzed at endpoint over a wide temperature range in a specific fluorescent color. Each bacterial target was identified by its pattern of hybridization to Lights-On/Lights-Off probes derived from molecular beacons. Complex mixtures of targets were also detected. Conclusions. All microbial targets were identified in samples containing low starting copy numbers of pathogen genomic DNA, both as individual targets and in complex mixtures. Significance and Impact of the Study. This assay uses new technology to achieve an advance in the field of molecular diagnostics: a single-tube multiplex assay for identification of pathogens commonly associated with sepsis.

Design of a single-tube, endpoint, linear-after-the-exponential-PCR assay for 17 pathogens associated with sepsis.

The goal of this study was to construct a single‐tube multiplex molecular diagnostic assay using linear‐after‐the‐exponential (LATE)‐PCR for the detection of 17 microbial pathogens commonly associated with septicaemia.

A Comprehensive Review of Linear Chain Iridium Complexes

The subject of linear chain materials which have unusual physical and chemical properties has been reviewed1 and discussed2,3 recently. A great deal of emphasis within these reviews has concentrated on the so-called Krogmann-type4 inorganic tetracyanoplatinate complexes and the 7, 7, 8, 8-tetracyano-p-quinodimethane (TCNQ) organic charge transfer materials because of their high anisotropic conductivities. However, the area of linear chain iridium complexes which have many of the common characteristics of the Krogmann salts has not been extensively reviewed.

Virtual Barcoding using LATE-PCR and Lights-On/Lights-Off probes: identification of nematode species in a closed-tube reaction.

Abstract The present study describes a rapid, universal, easy-to-use, closed-tube, non-sequencing method that should also be able to uniquely identify almost any animal species on earth. The approach, called Virtual Barcoding, is illustrated using five species of nematodes from three genera. Linear-After-The-Exponential (LATE) PCR was used to amplify a portion of the CO1 gene for each of five commercially available, beneficial species of soil nematodes. A set of ten low temperature Lights-On/Lights-Off consensus probes were included in the reaction mixture and were used at end-point to coat the accumulated single-stranded amplicon by dropping the temperature. Because each of the probes is mis-match tolerant, the temperature at which it hybridizes to its complementary region within the target is sequence dependent. As anticipated, each species had its own unique fluorescent signature in either three different colors, or a single color depending on which fluorophores were used to label the Lights-On probes. Each fluorescent signature was then mathematically converted to a species-specific Virtual Barcode.

Verification of monoplex and multiplex linear‐after‐the‐exponential PCR gene‐specific sepsis assays using clinical isolates

To verify monoplex and multiplex gene‐specific linear‐after‐the‐exponential polymerase chain reaction (LATE‐PCR) assays for identifying 17 microbial pathogens (i.e., Klebsiella sp., Acinetobacter baumannii, Staphylococcus aureus, Enterobacter sp., Pseudomonas aeruginosa, coagulase negative staphylococci, Enterococcus sp., Candida sp.) commonly associated with septicaemia using clinical isolates.

Design and construction of a single tube, quantitative endpoint, LATE-PCR multiplex assay for ventilator-associated pneumonia.

The goal of this study was to develop a molecular diagnostic multiplex assay for the quantitative detection of microbial pathogens commonly responsible for ventilator‐associated pneumonia (VAP) and their antibiotic resistance using linear‐after‐the‐exponential polymerase chain reaction (LATE‐PCR).