Detection Of Single-copy Genes Research Articles

Fluorescent labelling of in situ hybridisation probes through the copper-catalysed azide-alkyne cycloaddition reaction.

In situ hybridisation is a powerful tool to investigate the genome and chromosome architecture. Nick translation (NT) is widely used to label DNA probes for fluorescence in situ hybridisation (FISH). However, NT is limited to the use of long double-stranded DNA and does not allow the labelling of single-stranded and short DNA, e.g. oligonucleotides. An alternative technique is the copper(I)-catalysed azide-alkyne cycloaddition (CuAAC), at which azide and alkyne functional groups react in a multistep process catalysed by copper(I) ions to give 1,4-distributed 1,2,3-triazoles at a high yield (also called 'click reaction'). We successfully applied this technique to label short single-stranded DNA probes as well as long PCR-derived double-stranded probes and tested them by FISH on plant chromosomes and nuclei. The hybridisation efficiency of differently labelled probes was compared to those obtained by conventional labelling techniques. We show that copper(I)-catalysed azide-alkyne cycloaddition-labelled probes are reliable tools to detect different types of repetitive sequences on chromosomes opening new promising routes for the detection of single copy gene. Moreover, a combination of FISH using such probes with other techniques, e.g. immunohistochemistry (IHC) and cell proliferation assays using 5-ethynyl-deoxyuridine, is herein shown to be easily feasible.

Interview: From Down’s Syndrome to Basic Epigenetics and Back Again

Dr Jeanne Lawrence talks to Caroline Telfer, Commissioning Editor. Dr Jeanne Lawrence is an internationally recognized leader in the study of chromosome regulation by noncoding RNA and nuclear and genome organization. Her research bridges fundamental questions about genome regulation with clinical implications of recent advances in epigenetics. Her interest in chromosome structure and regulation has been a theme throughout her career and she has been honored for her work developing sensitive FISH technology for the detection of single copy genes, as well as RNAs. Her laboratory's publications include the initial demonstration of cell type-specific gene organization with nuclear subdomains; the novel biology of a noncoding RNA, XIST, which coats a whole X-chromosome to induce its silencing; and a new architectural role for a large noncoding RNA to scaffold a nuclear body. Her laboratory's work on epigenetic chromosome regulation in stem cells led to recent studies regarding unanticipated roles of repeat sequences in normal chromosome regulation and deregulation in cancer. Most recently, her laboratory has demonstrated a new approach to translate the basic mechanism of X-chromosome inactivation to correct a chromosomal dosage imbalance in patient-derived cells with trisomy 21 (Down's syndrome). Dr Lawrence has received awards from numerous agencies, including a Research Career Development Award from the National Center for Human Genome Research, career awards from the American Society of Cell Biology, the German Society for Biochemistry, the Muscular Dystrophy Association and a John Merck Fund Translational Research Award. She has served on the NIH National Advisory Council for Human Genome Research, numerous study sections and is currently a monitoring editor for the Journal of Cell Biology. Dr Lawrence has a BA in Biology and Music from Stephens College (MO, USA), a MS in Human Genetics and Genetic Counseling from Rutgers University (NJ, USA) and a PhD in Developmental Biology from Brown University (RI, USA). She is currently a Professor and Interim Chair of the Department of Cell and Developmental Biology at the University of Massachusetts Medical School (MA, USA).

Fluorescence in situ hybridization (FISH) mapping of single copy genes on Trichomonas vaginalis chromosomes

The highly repetitive nature of the Trichomonas vaginalis genome and massive expansion of various gene families has caused difficulties in genome assembly and has hampered genome mapping. Here, we adapted fluorescence in situ hybridization (FISH) for T. vaginalis, which is sensitive enough to detect single copy genes on metaphase chromosomes. Sensitivity of conventional FISH, which did not allow single copy gene detection in T. vaginalis, was increased by means of tyramide signal amplification. Two selected single copy genes, coding for serine palmitoyltransferase and tryptophanase, were mapped to chromosome I and II, respectively, and thus could be used as chromosome markers. This established protocol provides an amenable tool for the physical mapping of the T. vaginalis genome and other essential applications, such as development of genetic markers for T. vaginalis genotyping.

Detection of Single Copy Genes by Two-Pass Tyramide Signal Amplification Fluorescence in situ Hybridization (Two-Pass TSA-FISH) with Single Oligonucleotide Probes

In situ detection of functional genes is informative for understanding microbial physiology. Most methods of detecting functional genes employ multiple oligonucleotides or polynucleotide probes. However, single oligonucleotide probes are superior in terms of specificity and flexibility in probe design. Here we describe the detection of a single copy functional gene, the methyl coenzyme M reductase gene, in a methanogen by two-pass tyramide signal amplification-fluorescence in situ hybridization (two-pass TSA-FISH) with a single oligonucleotide probe without pre-amplification of target nucleic acids. Locked-nucleic-acid-incorporated DNA probes were employed to achieve high specificity and affinity. Although problems associated with non-removable nonspecific binding of the antibody could not be overcome completely, single copy gene detection was carried out with single mismatch descriminatable specificity; however, only around 15% of cells were detected. The detection rate increased when a multiple copy gene like rrn in Escherichia coli was targeted, indicating that a certain number of target molecules are necessary to achieve a high detection rate. Although possible applications of this technique to environmental samples remain restricted, the results presented the potential of gene detection by FISH with single oligonucleotide probes.

Branching Out of Single‐Molecule Fluorescence Spectroscopy: Challenges for Chemistry and Influence on Biology

AbstractFor Abstract see ChemInform Abstract in Full Text.

Branching Out of Single‐Molecule Fluorescence Spectroscopy: Challenges for Chemistry and Influence on Biology

In the last decade emerging single-molecule fluorescence-spectroscopy tools have been developed and adapted to analyze individual molecules under various conditions. Single-molecule-sensitive optical techniques are now well established and help to increase our understanding of complex problems in different disciplines ranging from materials science to cell biology. Previous dreams, such as the monitoring of the motility and structural changes of single motor proteins in living cells or the detection of single-copy genes and the determination of their distance from polymerase molecules in transcription factories in the nucleus of a living cell, no longer constitute unsolvable problems. In this Review we demonstrate that single-molecule fluorescence spectroscopy has become an independent discipline capable of solving problems in molecular biology. We outline the challenges and future prospects for optical single-molecule techniques which can be used in combination with smart labeling strategies to yield quantitative three-dimensional information about the dynamic organization of living cells.

Improving the accuracy of genetic diagnosis from single cells through analysis of real-time PCR signal kinetics

Improving the accuracy of genetic diagnosis from single cells through analysis of real-time PCR signal kinetics

Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities.

Spotted oligonucleotide microarrays potentially offer a wide scope of applications for microbial ecology, especially as they improve the flexibility of design and the specificity of detection compared to PCR product based microarrays. Sensitivity, however, was expected to be problematic, as studies with the more sensitive PCR-based cDNA microarrays indicate that only genes from populations contributing to more than 5% of the community DNA can be detected. We evaluated several parameters to increase sensitivity and then tested applicability for bacterial functional genomics. The optimal parameters were the use of 5'-C6-amino-modified 70-mers printed on CMT-GAPS II substrates at a 40 micro M concentration combined with the use of Tyramide Signal Amplification labelling. This protocol allowed detection of single copy genes belonging to an organism contributing to 1% or more of the total community. To demonstrate its application, we detected the specific aromatic oxygenase genes in a soil community degrading polychlorinated biphenyls (PCBs). This increase in sensitivity is important if oligonucleotide microarrays are to be used for simultaneous monitoring of a range of functions performed by different microorganisms in the environment.

Urea substitutes toxic formamide as destabilizing agent in nucleic acid hybridizations with RNA probes.

Since their introduction some three decades ago, methods for hybridization analysis of nucleic acids immobilized on solid supports have evolved to improve the sensitivity, speed, and convenience of their application. However, in many cases these methods still require the use of solutions containing formamide, a recognized hazardous solvent with potential toxicity. Here, we have compared the efficiency of urea to that of formamide as denaturing agent in nucleic acid hybridization with RNA probes. We show that urea at concentrations of 2-4 molar in solution performs as good as 50% formamide to reduce heterologous background hybridization in Northern blotting experiments realized at 68 degrees C. Presence of urea at higher concentrations resulted in reduced hybridization sensitivity, possibly due to increased viscosity. When tested in Southern blot analysis of genomic DNA, our results revealed that the use of urea in hybridization solution is also suitable to carry out single-copy gene detection. Together, these findings show that urea can efficiently and safely replace formamide in solutions.

Nonradioactive labeling of large DNA fragments for genome walking, RFLP and northern blot analysis.

In this report, we present a simple nonradioactive labeling procedure for DNA fragments of high specific labeling density that can be used for a variety of applications. The protocol is based on the universal mono-functional platinum reagent for chemical digoxigenin (DIG) labeling of nucleic acids. The labeling protocol was optimized for large DNA templates as complete bacterial artificial chromosomes (BAC). Variations of incubation time and temperature improved the labeling density such that about 30% of the nucleotides were DIG-modified within 30 min. Furthermore, the refined procedure generates in a single-tube reaction and without prior digestion-labeled DNA fragments of 0.5-4.0 kb from a 130-kb template. Hybridization experiments were performed on Southern and northern blots and allowed the detection of single copy genes in 2.5 micrograms genomic DNA from Arabidopsis thaliana, which has a haploid genome size of 0.13 pg (ca. 120 Mb) and medium expressed transcripts from 0.8 microgram poly(A)+ RNA, respectively. The extremely high specific labeling density, the stability and the universal application of the probe generated with the platinum reagent makes this method a useful alternative to classical radioactive nuclei acids labeling techniques.

Detection of single-copy genes in DNA from transgenic plants by nonradioactive Southern blot analysis.

Improvements to the sensitivity, speed, and reproducibility of digoxigenin (DIG)-labeled probes and chemiluminescent substrates makes these compounds increasingly popular to detect nucleic acids. High sensitivity and low background are essential in Southern blot analysis, particularly with plant DNA. This article describes a nonradioactive system to detect single-copy genes in transgenic plants. Labeling using the polymerase chain reaction (PCR) was employed to produce highly sensitive and reusable DIG-labeled probes. The background was reduced by immobilizing the DNA onto nylon filters by alkaline transfer and by minimized gel handling; the signal-to-noise ratio was improved by modification of the detection procedure.

Primed in situ labeling (PRINS). A fast method for in situ labeling of nucleic acids.

PRimed IN Situ labeling (PRINS) is a fast and sensitive alternative to fluorescence in situ hybridization (FISH) for identification of chromosome aberrations. In this article, we present the detailed protocols for detection of repeat sequences using oligonucleotides or fragments of cloned probes as primers for PRINS. We describe a multicolor PRINS procedure for simultaneous visualization of more probes in different colors on a metaphase preparation, and a PRINS-painting procedure, which combines PRINS and chromosome painting. Finally, a protocol for detection of single-copy genes is presented.

Detection of single-copy genes by nonisotopic in situ hybridization on human chromosomes.

A technique of in situ hybridization on metaphase chromosomes with biotinylated DNA probes is described. This technique was used to localize unique DNA sequences on chromosomes and allowed a localization of two probes 1.8 and 1.3 kb long. The hybridization signal appears like two, twin, spots on the two sister chromatids, allowing a clear distinction from the background. Moreover a chromosomal localization is possible by counting a relatively small number of mitoses compared with the technique using 3H-labeled DNA probes.

Colormetric detection of horseradish peroxidase labelled DNA using a new chromogen system

A new chromogen system is described for the detection of horseradish peroxidase (E.C. 1.11.1.7) labelled DNA. Lambda DNA was used as a model and the new system compared favourably with an existing method. The results show the technique should be suitable for single copy gene detection with a lower detection limit of 1–5pg.

Novel biotinylated nucleotide--analogs for labeling and colorimetric detection of DNA.

A series of dATP and dCTP nucleotide analogs have been synthesized which are modified by attachment of aliphatic linkers containing a functional group to the amino-nitrogen at the hydrogen bonding positions of the bases, that is, at the 6-position of adenine and the 4-position of cytosine. These nucleotides are incorporated into DNA probes by standard nick-translation protocols. DNA probes labeled with biotin derivatives of these nucleotides are effectively hybridized to target DNA sequences and can be detected by a streptavidin and calf intestinal alkaline phosphatase conjugate with a sensitivity (0.25 pg DNA) sufficient for reproducible and rapid detection of single copy genes in a Southern blot of mammalian DNA. Also, a procedure has been developed to allow reprobing of nylon filters that have been hybridized with biotinylated probes and developed with the streptavidin/alkaline phosphatase conjugate and a standard dye system.

High-efficiency preparation of DNA from limiting quantities of eukaryotic cells for hybridization analysis

This report describes a DNA preparation method which allows the detection of single-copy genes in samples of as few as 6000 eukaryotic cells. The technique uses proteinase K digestion in detergent and low-gelationtemperature agarose followed by solidification of the agarose and removal of the detergent by diffusion. RNase and restriction enzyme digestion are carried out in solution after remelting the agarose. The procedure can be performed successfully with mammalian cells in suspension, with parasitic protozoa and with pieces of mammalian tissue weighing less than l mg. Numerous samples can be processed simultaneously using frozen as well as fresh material.

Detection of sickle-cell mutation by electrophoresis of partial RNA:DNA hybrids following solution hybridization

We have developed a method in which partially single-stranded (ss) DNA molecules containing a defined region of duplex RNA:DNA are electrophoretically separated in agarose gels. The partial hybrids are formed by solution hybridization with a uniform length RNA probe complementary to part of the DNA sequence of interest. Following hybridization, the RNA/DNA mixture is fractionated by agarose gel electrophoresis at high temperature to minimize intrastrand base pairing which causes mobility heterogeneity. Not requiring the steps of DNA transfer from the gel to a solid support and subsequent probing, pre-electrophoretic hybridization allows the direct identification of single-copy fragments. Conditions for the detection of single-copy genes in human DNA digested with specific restriction endonucleases were developed and applied to the diagnosis of sickle-cell disease. This method should be applicable for the analysis of DNAs of high complexity where the presence of DNA polymorphisms and interspersed repeated DNA sequences often make impossible the creation of complete RNA:DNA hybrids.