Non-radioactive chemical sequencing of biotin labelled DNA.

Methods for the nonradioactive chemical sequencing of DNA are described. A biotin marker molecule, attached chemically to an oligonucleotide primer or enzymatically in an endfilling reaction of restriction enzyme sites, is stable during the base-specific chemical modification and strand scission reactions. Following fragment separation by direct blotting electrophoresis, the membrane bound sequence pattern can be visualized by a streptavidin-bridged enzymatic color reaction. The biotin labeling is also applicable for DNA sequencing by random degradation of phosphothioates, thus showing to be a universal label for nonradioactive DNA sequencing.     

A new method of synthesis of fluorescently labelled oligonucleotides and their application in DNA sequencing.

A new approach to the chemical synthesis of oligodeoxynucleotides bearing reporter functional groups at base residues of 3'-end nucleosides is reported. Applications of the 3'-end fluorescently labelled primers for automated DNA sequencing are shown.     

Amplification of fluorescently labelled DNA within gram-positive and acid-fast bacteria.

Representative organisms from a variety of Gram-positive genera were subjected to varying regimes in order to optimise the intracellular amplification of DNA. The bacteria were subjected to treatments with paraformaldehyde, muramidases and mild acid hydrolysis to discover which regime made each organism permeable to the amplification reagents yet allowed retention of the fluorescein-labelled amplified products within the cell. Scanning electron micrographs were used to corroborate the effectiveness of the treatments, as seen by fluorescent photomicrographs, with the damage caused to the bacterial walls. A combination of mutanolysin and lysozyme was found most effective for Bacillus cereus, whereas permeabilisation of Streptomyces coelicolor, Lactococcus lactis and Clostridium sporogenes was most effective when exposed to lysozyme only. Surprisingly, direct amplification with no pre-treatment gave the brightest fluorescence in Mycobacterium phlei. Comparing the techniques of whole cell PCR, primed in situ labelling (PRINS), and cycle PRINS showed that under the conditions used the strongest intensity of fluorescence was obtained with in situ PCR; only L. lactis and M. phlei produced signals with cycle PRINS, fluorescence was not seen for any of the organisms with PRINS.     

Non-radioactive automated sequencing of oligonucleotides by chemical degradation

A non-radioactive sequencing of fluorescently labelled oligonucleotides by solid-phase chemical degradation is described. Although non-radioactive methods have been reported for the dideoxy chain termination technique, such a method has not yet been developed for the chemical degradation sequencing of DNA fragments. A 21-mer fluorescein labelled M13 sequencing primer was sequenced in an on-line automated system in about 30 minutes. The fluorescent dye and its bond to the oligonucleotide were stable during the chemical reactions used for the base specific degradations. As the sequence is determined on-line during electrophoresis, reloading and running 10 fragments simultaneously allows us to use one gel for sequencing of about 50 different oligonucleotides.     

Preparation of fluorescently labelled hybrid histone octamers

Labelling hybrid histone octamers (the Cys variant of histone H4 replaced histone H4 in the chicken erythrocyte octamer) with the fluorescent probe 5-(2(iodoacetyl)aminoethyl)aminonapthalene- 1-sulfonic acid, IAEDANS, resulted in significant non-specific incorporation of label. Fluorescently labelled hybrid histone octamers were prepared by reconstitution methodology after labelling the isolated histone Cys-H4 and separation of specifically and non-specifically labelled histone. Core particles prepared from these octamers have identical thermal denaturation to unlabelled core particles demonstrating that the incorporation of a fluorescent probe at this site has no overall effect on either histone-histone or histone-DNA interactions. DNase 1 digestion of 32P end-labelled fluorescent core particles yielded the anticipated asymmetric cutting pattern with a 10 bp interval between fragments. Comparison of the cutting pattern with those previously obtained in these laboratories for both polyglutamic acid reconstituted and 'native' core particles demonstrated that fluorescent core particles had an enhanced susceptibility to digestion at site 7.     

A novel type of cloning vectors for ultrarapid chemical degradation sequencing of DNA

The construction and evaluation of a novel type of chemical sequencing vectors (pCSV) is described. These small plasmids bear a unique asymmetric restriction site suitable for direct single-end labeling by filling-in polymerization with a selected radiolabeled nucleoside triphosphate. Thus, a secondary cleavage reaction or segregation step is rendered superfluous. Sequencing gels can be read unambiguously starting from the 3′ penultimate nucleotide. pCSV03 and pCSV27 are prototypes of such sequencing plasmids based on BstEII as the labeling site. In its proximity, restriction sites are present that allow subcloning of the DNA fragments to be sequenced. Approaches to random and progressive sequencing using these vectors are discussed. pCSV31 has two Tth111I sites that allow single-end labeling of inserts on either strand by the use of different labeled nucleoside triphosphates. Thus, bidirectional sequencing of larger inserts (>500 bp) is possible.     

Determination of the mitotic index by microinjection of fluorescently labelled tubulin

The microneedle injection technique is one of the most established procedures for the introduction of proteins into living cells. To analyse injected proteins which are important in cell cycle progression it is often necessary to determine the mitotic index. Measuring the mitotic index after microinjection is complicated because only a limited number of cells of the whole cell population is microinjected. Therefore, we attempted to establish a new method to determine the mitotic index using microinjection of fluorescently labelled alpha/beta-tubulin into mammalian cells which allows to monitor the injected cells simultaneously with the determination of the mitotic index. We demonstrated that fluorescently labelled tubulin incorporates efficiently into the mitotic spindle apparatus. Fluorescence remains stable for several hours which is sufficient to observe the progression of cells through the M-phase of the cell cycle. The determination of the mitotic index with the method presented here gave similar results to those determined using other methods. With this method also different stages of mitosis can be visualized by analysing various steps of spindle formation. Thus, this rapid method allows the monitoring of the injected cells after microneedle injection and simultaneously the determination of the mitotic index.     

Automated four-color DNA sequencing using primers assembled by hexamer ligation

A procedure based on the assembly of sequencing primers by hexamer ligation and then using them in automated DNA sequencing is described. This method is based on a four-color fluorescent terminator chemistry. Sequencing ladders were analyzed using an ABI 373 DNA sequencer (Applied Biosystems, Foster City, CA, USA). The best results were obtained for primers assembled by ligation of four to ten hexamers. The accuracy of the method was estimated to be 99.5% up to 400 nt of the read sequence, and somewhat lower at 400–600 nt.     

DNA hybridization detection in a microfluidic channel using two fluorescently labelled nucleic acid probes

A conceptually new technique for fast DNA detection has been developed. Here, we report a fast and sensitive online fluorescence resonance energy transfer (FRET) detection technique for label-free target DNA. This method is based on changes in the FRET signal resulting from the sequence-specific hybridization between two fluorescently labelled nucleic acid probes and target DNA in a PDMS microfluidic channel. Confocal laser-induced microscopy has been used for the detection of fluorescence signal changes. In the present study, DNA hybridizations could be detected without PCR amplification because the sensitivity of confocal laser-induced fluorescence detection is very high. Two probe DNA oligomers (5'-CTGAT TAGAG AGAGAA-TAMRA-3' and 5'-TET-ATGTC TGAGC TGCAGG-3') and target DNA (3'-GACTA ATCTC TCTCT TACAG GCACT ACAGA CTCGA CGTCC-5') were introduced into the channel by a microsyringe pump, and they were efficiently mixed by passing through the alligator teeth-shaped PDMS microfluidic channel. Here, the nucleic acid probes were terminally labelled with the fluorescent dyes, tetrafluororescein (TET) and tetramethyl-6-carboxyrhodamine (TAMRA), respectively. According to our confocal fluorescence measurements, the limit of detection of the target DNA is estimated to be 1.0 x 10(-6) to 1.0 x 10(-7)M. Our result demonstrates that this analytical technique is a promising diagnostic tool that can be applied to the real-time analysis of DNA targets in the solution phase.     

Automated template quantification for DNA sequencing facilities.

The quantification of plasmid DNA by the PicoGreen dye binding assay has been automated, and the effect of quantification of user-submitted templates on DNA sequence quality in a core laboratory has been assessed. The protocol pipets, mixes and reads standards, blanks and up to 88 unknowns, generates a standard curve, and calculates template concentrations. For pUC19 replicates at five concentrations, coefficients of variance were 0.1, and percent errors were from 1% to 7% (n=198). Standard curves with pUC19 DNA were nonlinear over the 1 to 1733 ng/microL concentration range required to assay the majority (98.7%) of user-submitted templates. Over 35,000 templates have been quantified using the protocol. For 1350 user-submitted plasmids, 87% deviated by >or=20% from the requested concentration (500 ng/microL). Based on data from 418 sequencing reactions, quantification of user-submitted templates was shown to significantly improve DNA sequence quality. The protocol is applicable to all types of double-stranded DNA, is unaffected by primer (1 pmol/microL), and is user modifiable. The protocol takes 30 min, saves 1 h of technical time, and costs approximately $0.20 per unknown.     

Synthesis of fluorescently labelled and internally quenched UDP-Gal probes

The preparation of fluorescently labelled and internally quenched UDP-Gal probes bearing a fluorescence emitter and a quencher is described. The rate of transfer using several galactosyltransferases was examined. Our results demonstrate that galactose-modified, sugar-nucleotide-modified and double modified UDP-Gal analogues are recognized as weak substrates by blood group B alpha-(1-->3) galactosyltransferase, alpha-(1-->3) galactosyltransferase and milk bovine beta-(1-->4) galactosyltransferase.     

Automated DNA sequencing and analysis of the human genome

In the past few years, striking advances have been made in automating DNA sequence analysis. Currently, efforts are underway to automate and improve DNA purification, mapping, and data processing procedures. The predictable advances in these technologies should soon place us in a position to sequence the entire human genome. The information derived from this project will have profound implications for basic biology and clinical medicine alike.     

Biosynthetic incorporation of fluorescently labelled fatty acids in Escherichia coli

Escherichia coli cells were cultivated in a medium containing 1-pyrene butanoic acid, a fluorescent probe. Total lipids were extracted from the cells, and the extract was separated by thin-layer chromatography. The fluorescent fractions were examined using spectrofluorimetry. The starting 1-pyrene butanoic acid was shown to be biosynthetically incorporated into the bacterial lipid. Four fluorescent fractions appeared as a result; the fractions were derivatives of this compound modified in the chromophore and the fatty acid chain. The results indicate that the formation of 1-pyrene butanoic acid fluorescent metabolites can be used for studying the oxidation-reduction systems of the bacterium.     

A facile method to prepare C-terminal fluorescently labelled peptides by an Fmoc strategy

Summary Spectrophotometric peptide probes, derivatized at the C-terminus, are conveniently prepared by means of an Fmoc solid-phase strategy. Using a resin such as Sasrin, the fully protected peptide can be cleaved from the resin with hydrazine, yielding the protected peptide-hydrazide which is subsequently oxidized to the azide. An amino-containing chromophore or fluorophore such as 5-[(2-aminoethyl)-amino]-naphthalene sulfonic acid (EDANS) can be coupled directly to this activated carboxyl group. This allows for specific placement of the fluorophore at the C-terminal carboxyl group in the presence of trifunctional amino acids.