Biomedical subjects

A Holmgren

Publications and source records attributed to A Holmgren.

At least 19 recordsLinked to original sources

PubMed2005

Role of thioredoxin in the response of normal and transformed cells to histone deacetylase inhibitors.

This study examines the basis of resistance and sensitivity of normal and transformed cells to histone deacetylase inhibitor (HDACi)-induced cell death, specifically the role of caspases and thioredoxin (Trx). An important attribute of HDACis is that they induce cancer cell death at concentrations to which normal cells are relatively resistant, making them well suited for cancer therapy. The mechanism underlying this selectivity has not been understood. In this study we found that the HDACi suberoylanilide hydroxamic acid (SAHA) and MS-275, a benzamide, cause an accumulation of reactive oxygen species (ROS) and caspase activation in transformed but not normal cells. Inhibition of caspases does not block HDACi-induced cell death. These studies provide a possible mechanism that can explain why normal but not certain transformed cells are resistant to HDACi-induced cell death. The HDACi causes an increase in the level of Trx, a major reducing protein for many targets, in normal cells but not in transformed cells. The SAHA-induced increase in Trx activity in normal cells is associated with no increase in ROS accumulation. Transfection of transformed cells with Trx small interfering RNA caused a marked decrease in the level of Trx protein with an increase in ROS, a decrease in cell proliferation, and an increase in sensitivity to SAHA-induced cell death. Thus, Trx, independent of the caspase apoptotic pathway, is an important determinant of resistance of cells to HDACi-induced cell death.

Apoptosis↗

PubMed2005

Thiol redox control via thioredoxin and glutaredoxin systems.

The Trx (thioredoxin) and Grx (glutaredoxin) systems control cellular redox potential, keeping a reducing thiol-rich intracellular state, which on generation of reactive oxygen species signals through thiol redox control mechanisms. Here, we give a brief overview of the human Trx and Grx systems. The main part focuses on our current knowledge about mitochondrial Grx2, which facilitates mitochondrial redox homoeostasis during oxidative stress-induced apoptosis.

Animals↗

PubMed2005

Abnormally high concentrations of amphetamine in blood of impaired drivers.

We present a case series (N = 46) of individuals apprehended in Sweden for driving under the influence of drugs (DUID). These cases were selected because the concentrations of amphetamine in blood were abnormally high (> 5.0 mg/L), the highest being 17 mg/L. In comparison, the median blood-amphetamine concentration in a population of DUID offenders (N = 6,613) was 0.70 mg/L. Among the DUID suspects with extremely high blood-amphetamine concentrations there were 38 men (83%) with mean age of 37.8 y (SD 6.8 y) and 8 women (17%) with a mean age of 34.1 y (SD 4.3 y). All had previously been registered in our database (mean 12 times, median 9 times) for drug-related offences, including DUID. The concentration of amphetamine in blood of female offenders was slightly higher than the concentration in male offenders (6.6 mg/L vs. 5.8 mg/L), although this difference was not statistically significant (p > 0.05). The drugs other than amphetamine most frequently encountered in the blood samples were tetrahydrocannabinol and benzodiazepines (diazepam and nordiazepam). The commonest signs of drug use reported by the arresting police officers were bloodshot and glazed (watery) eyes, restlessness, talkativeness, exaggerated reflexes and slurred speech. Unsteady gait and dilated pupils were observed in some but not all individuals. These very high concentrations of amphetamine were tolerated without any fatalities indicating a pronounced adaptation to the pharmacologic effects of this central stimulant. Anecdotal information indicated that those with the very highest concentrations of amphetamine in blood had swallowed the drug to prevent being apprehended in possession of an illicit substance.

Adult↗

PubMed2004

High concentrations of diazepam and nordiazepam in blood of impaired drivers: association with age, gender and spectrum of other drugs present.

A zero-concentration limit for controlled scheduled drugs in the blood of motorists was introduced in Sweden in 1999 and the annual number of arrests for driving under the influence of drugs (DUID) has since increased eight-fold. However, for prescription drugs that might cause impairment (e.g. benzodiazepines) additional proof is needed to justify prosecution, such as whether the medication was being misused. Over a 2-year period, we found 94 cases of DUID in which the concentrations of diazepam in blood was 1.1 microg/g or more. Diazepam (D) and nordiazepam (ND) were determined in whole blood by capillary gas chromatography with a limit of quantitation of 0.05 microg/g for each compound. The mean (median) and maximum concentrations of D were 2.0 microg/g (1.7 microg/g) and 7.8 microg/g and the corresponding ND concentrations were 1.5 microg/g (1.0 microg/g) and 7.6 microg/g, respectively. The concentration of D in blood exceeded 2 microg/g in 21% of cases and was over 3.0 microg/g in 11% of cases. D and ND were the only drugs present in eight cases (seven men and one women) and in another five cases ethanol was present at concentrations ranging from 0.81 to 1.98 mg/g. Polydrug use was very common in these DUID suspects and D and ND coexisted with amphetamine in 20% of cases, tetrahydrocannabinol in 18% of cases and with both these illicit drugs in 12% of cases. The next most prevalent drug combination was D, ND and morphine (mostly derived from heroin), seen in 13% of cases. Other psychoactive prescription drugs were identified in blood including alprazolam, flunitrazepam, oxazepam, zolpidem and zopiclone. This case series of DUID suspects demonstrate the high frequency of polydrug use showing preference for illicit drugs like amphetamine, cannabis and heroin, in that order. Furthermore, Swedish traffic delinquents frequently overdose with prescription drugs as exemplified here by unusually high concentrations of D and its active metabolite ND.

Adolescent↗

PubMed2004

Direct observation of a self-assembled monolayer of heptyl xanthate at the germanium/water interface: a polarized FTIR study.

The adsorption of heptyl xanthate on germanium has been studied by the attenuated total reflection (ATR) technique. Polarized infrared light was used in situ to determine the average orientation of the alkyl chain in heptyl xanthate adsorbed at the germanium/solution interface. Spectra reveal the formation of closely packed xanthate ions with the alkyl chains in the all-trans conformation. The average tilt angle of the alkyl chains of heptyl xanthate was approximately 47 degrees from the surface normal.

Journal Article↗

PubMed2004

Electric chips for rapid detection and quantification of nucleic acids.

A silicon chip-based electric detector coupled to bead-based sandwich hybridization (BBSH) is presented as an approach to perform rapid analysis of specific nucleic acids. A microfluidic platform incorporating paramagnetic beads with immobilized capture probes is used for the bio-recognition steps. The protocol involves simultaneous sandwich hybridization of a single-stranded nucleic acid target with the capture probe on the beads and with a detection probe in the reaction solution, followed by enzyme labeling of the detection probe, enzymatic reaction, and finally, potentiometric measurement of the enzyme product at the chip surface. Anti-DIG-alkaline phosphatase conjugate was used for the enzyme labeling of the DIG-labeled detection probe. p-Aminophenol phosphate (pAPP) was used as a substrate. The enzyme reaction product, p-aminophenol (pAP), is oxidized at the anode of the chip to quinoneimine that is reduced back to pAP at the cathode. The cycling oxidation and reduction of these compounds result in a current producing a characteristic signal that can be related to the concentration of the analyte. The performance of the different steps in the assay was characterized using in vitro synthesized RNA oligonucleotides and then the instrument was used for analysis of 16S rRNA in Escherichia coli extract. The assay time depends on the sensitivity required. Artificial RNA target and 16S rRNA, in amounts ranging from 10(11) to 10(10) molecules, were assayed within 25 min and 4 h, respectively.

Biosensing Techniques↗

PubMed2003

Immunohistochemical determination of thioredoxin and glutaredoxin distribution in the human cervix, and possible relation to cervical ripening.

Thioredoxin (Trx) and glutaredoxin (Grx) are dithiol redox enzymes, catalyzing general thiol-disulfide oxidoreductions apart from being hydrogen donors for ribonucleotide reductase, an enzyme essential for DNA synthesis. In mammals, isoenzymes of Trx and Grx are found in the cytoplasm (Trx1 and Grx1) or in mitochondria (Trx2 and Grx2). Trx and Grx play a role in cellular defence against oxidative stress and in redox regulation of cellular function. The localization and levels of human Trx1 and human Grx1 have been determined in the human cervix by immunohistochemistry and image analysis. Cervical biopsies were obtained from five non-pregnant, five term pregnant and five postpartum women. The levels of both Trx1 and Grx1 were increased in the nuclei (after translocation from the cytoplasm) of stromal cells in cervices from the term pregnant group as compared to the non-pregnant group, but the levels in the postpartum group did not differ significantly from those of the other two groups. These results are in agreement with our previous data on the mRNA expression of these two redox enzymes. The increased levels of the redox enzymes in term pregnancy suggest that they can be regulating factors involved in the process of cervical ripening, e.g. transcription factors and enzymes. Secreted Trx may participate in removing inhibitors of collagen-degrading metalloproteinases.

Adult↗

PubMed2002

Poorly humified peat as an adsorbent for metals in wastewater.

Metal adsorption and surface charge determinations were performed previously on well-characterised Sphagnum and Carex peat samples. The aim of this investigation was to determine metal adsorption from complex wastewaters onto these peat samples and compare it to the adsorption onto peat granules, clinoptilolite, glauconite and a flue dust from steel production. A sulphide mine leachate, a landfill leachate and a laundry wastewater were chosen, giving a variation in pH, ionic strength, total organic carbon and concentrations of metals. Metal adsorption was determined in batch and column experiments. The wastewater composition was of great importance for metal removal efficiency, mainly due to the difference in dominating metal species. In the sulphide mine leachate, containing free metal ions, a high metal adsorption was observed onto both peat and inorganic adsorbents. In the landfill leachate the metals formed carbonate and organic complexes and a low metal removal was achieved. Contrary to the leachates, the laundry wastewater contained suspended particles. The high amount of metals removed, 80% of the Cu and 30-60% of the Zn concentration, was probably withdrawn bound to the particle fraction. The highest removal of metal ions was obtained in the sulphide mine leachate with Carex peat, removing 97-99% of the Zn and 85-100% of the Cu content. The Sphagnum peat sample removed 37-77% of the Zn and 80-100% of the Cu content. The differences found between Sphagnum and Carex peat were attributed to the original chemistry of the plant material and the habitat conditions at the time of peat formation. Generally, the combination of glauconite or clinoptilolite with the peat samples in column experiments gave a minor improvement in metal removal.

Adsorption↗

PubMed2002

Immunohistochemical localization of glutaredoxin and thioredoxin in human endometrium: a possible association with pinopodes.

The human endometrium is only receptive for blastocyst implantation during a short period of the menstrual cycle. Pinopodes have been suggested to be markers of uterine receptivity, but little is known about their function and the biochemical processes taking place in them. In this study, we have examined the presence of glutaredoxin (Grx) and thioredoxin (Trx) and their co-localization with pinopodes in the normal human endometrium. Endometrial biopsies were obtained from fertile women with normal menstrual cycles. The biopsies were examined by scanning electron microscopy for detection of pinopodes and by immunohistochemistry for the expression of Grx and Trx. The pinopodes showed strong immunostaining for Grx. Increasing levels of Grx immunoreactivity were seen in the luminal and glandular epithelial cells concomitant with pinopode formation. Trx immunostaining was most intense in the ciliated cells of the luminal and glandular epithelium, while the staining was moderate to strong in a majority of the other cells, both epithelial and stromal. Trx levels did not change during the secretory phase of the cycle. The intense immunostaining concomitant with the presence of pinopodes suggests that Grx plays an important role during implantation, possibly by protecting the epithelial cells from apoptotic actions of the trophoblast cells.

Adult↗

PubMed2001

Analysis of the inhibition of mammalian thioredoxin, thioredoxin reductase, and glutaredoxin by cis-diamminedichloroplatinum (II) and its major metabolite, the glutathione-platinum complex.

Several studies have demonstrated a correlation between cellular toxicity of cis-diamminedichloroplatinum (II) (cisplatin, CDDP) and inhibited intracellular activity of the thioredoxin system, i.e., thioredoxin (Trx), thioredoxin reductase (TrxR), and NADPH. Conversely, increased cellular activity of the Trx system confers resistance to CDDP. In this study, we have analyzed the interaction of CDDP with Trx and TrxR in order to clarify the mechanism. The inhibition with time-dependent kinetics by CDDP of NADPH-reduced (but not oxidized) TrxR was irreversible, strongly suggesting covalent modification of the reduced selenocysteine-containing active site. Assuming second order kinetics, the rate constant of TrxR inhibition by CDDP was 21 +/- 3 M(-1) x s(-1). Transplatin was found to be an even more efficient inhibitor, with a second order rate constant of 84 +/- 22 M(-1) x s(-1), whereas carboplatin (up to 1 mM) gave no inhibition of the enzyme under the same conditions. Escherichia coli Trx or human or bacterial glutaredoxin (Grx) activities were in comparison only slightly or not at all inhibited by either CDDP, transplatin, or carboplatin. However, glutaredoxins were found to be inhibited by the purified glutathione adduct of cisplatin, bis-(glutathionato)platinum(II) (GS-Platinum complex, GS-Pt), with an IC50 = 350 microM in the standard beta-hydroxyethyl disulfide-coupled assay for human Grx. Also the mammalian Trx system was inhibited by GS-Pt with similar efficiency (IC(50) = 325 microM), whereas neither the E. coli Trx system nor glutathione reductase were inhibited. Formation of GS-Pt is a major route for cellular elimination of CDDP. The fact that GS-Pt inhibits the mammalian Trx as well as Grx systems shows that CDDP may exert effects at several stages of its metabolism, including after conjugation with GSH, which are intimately linked with the cellular disulfide/dithiol redox regulatory systems.

Animals↗

PubMed2001

Three-dimensional structure of a mammalian thioredoxin reductase: implications for mechanism and evolution of a selenocysteine-dependent enzyme.

Thioredoxin reductases (TrxRs) from mammalian cells contain an essential selenocysteine residue in the conserved C-terminal sequence Gly-Cys-SeCys-Gly forming a selenenylsulfide in the oxidized enzyme. Reduction by NADPH generates a selenolthiol, which is the active site in reduction of Trx. The three-dimensional structure of the SeCys498Cys mutant of rat TrxR in complex with NADP(+) has been determined to 3.0-A resolution by x-ray crystallography. The overall structure is similar to that of glutathione reductase (GR), including conserved amino acid residues binding the cofactors FAD and NADPH. Surprisingly, all residues directly interacting with the substrate glutathione disulfide in GR are conserved despite the failure of glutathione disulfide to act as a substrate for TrxR. The 16-residue C-terminal tail, which is unique to mammalian TrxR, folds in such a way that it can approach the active site disulfide of the other subunit in the dimer. A model of the complex of TrxR with Trx suggests that electron transfer from NADPH to the disulfide of the substrate is possible without large conformational changes. The C-terminal extension typical of mammalian TrxRs has two functions: (i) it extends the electron transport chain from the catalytic disulfide to the enzyme surface, where it can react with Trx, and (ii) it prevents the enzyme from acting as a GR by blocking the redox-active disulfide. Our results suggest that mammalian TrxR evolved from the GR scaffold rather than from its prokaryotic counterpart. This evolutionary switch renders cell growth dependent on selenium.

Amino Acid Sequence↗

PubMed2001

Solution structure of Escherichia coli glutaredoxin-2 shows similarity to mammalian glutathione-S-transferases.

Glutaredoxin 2 (Grx2) from Escherichia coli is distinguished from other glutaredoxins by its larger size, low overall sequence identity and lack of electron donor activity with ribonucleotide reductase. However, catalysis of glutathione (GSH)-dependent general disulfide reduction by Grx2 is extremely efficient. The high-resolution solution structure of E. coli Grx2 shows a two-domain protein, with residues 1 to 72 forming a classical "thioredoxin-fold" glutaredoxin domain, connected by an 11 residue linker to the highly helical C-terminal domain, residues 84 to 215. The active site, Cys9-Pro10-Tyr11-Cys12, is buried in the interface between the two domains, but Cys9 is solvent-accessible, consistent with its role in catalysis. The structures reveal the hither to unknown fact that Grx2 is structurally similar to glutathione-S-transferases (GST), although there is no obvious sequence homology. The similarity of these structures gives important insights into the functional significance of a new class of mammalian GST-like proteins, the single-cysteine omega class, which have glutaredoxin oxidoreductase activity rather than GSH-S-transferase conjugating activity. E. coli Grx 2 is structurally and functionally a member of this new expanding family of large glutaredoxins. The primary function of Grx2 as a GST-like glutaredoxin is to catalyze reversible glutathionylation of proteins with GSH in cellular redox regulation including stress responses.

Amino Acid Sequence↗

PubMed2001

Structural basis for the thioredoxin-like activity profile of the glutaredoxin-like NrdH-redoxin from Escherichia coli.

NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. The crystal structure of recombinant Escherichia coli NrdH-redoxin in the oxidized state has been determined at 1.7 A resolution by multiwavelength anomalous diffraction. NrdH-redoxin belongs to the thioredoxin superfamily and is structurally most similar to E. coli glutaredoxin 3 and phage T4 glutaredoxin. The angle between the C-terminal helix alpha3 and strand beta4, which differs between thioredoxin and glutaredoxin, has an intermediate value in NrdH-redoxin. The orientation of this helix is to a large extent determined by an extended hydrogen-bond network involving the highly conserved sequence motif (61)WSGFRP(D/E)(67), which is unique to this subclass of the thioredoxin superfamily. Residues that bind glutathione in glutaredoxins are in general not conserved in NrdH-redoxin, and no glutathione-binding cleft is present. Instead, NrdH-redoxin contains a wide hydrophobic pocket at the surface, similar to thioredoxin. Modeling studies suggest that NrdH-redoxin can interact with E. coli thioredoxin reductase at this pocket and also via a loop that is complementary to a crevice in the reductase in a similar manner as observed in the E. coli thioredoxin-thioredoxin reductase complex.

Amino Acid Sequence↗

PubMed2001

EPR investigation of the active site of recombinant human 5-lipoxygenase: inhibition by selenide.

Lipoxygenases are a group of non-heme iron dioxygenases which catalyze the formation of lipid hydroperoxides from unsaturated fatty acids. 5-Lipoxygenase (5LO) is of particular interest for formation of leukotrienes and lipoxins, implicated in inflammatory processes. In this study, electron paramagnetic resonance (EPR) spectroscopy was used to investigate the active site iron of purified recombinant human 5-lipoxygenase (5LO), and to explore the action of selenide on 5LO. After oxidation by lipid hydroperoxides, 5LO exhibited axial EPR spectra typified by a signal at g = 6.2. However, removal of the lipid hydroperoxides, their metabolites, and the solvent ethanol from the samples resulted in a shift to more rhombic EPR spectra (g = 5.17 and g = 9.0). Thus, many features of 5LO and soybean lipoxygenase-1 EPR spectra were similar, indicating similar flexible iron ligand arrangements in these lipoxygenases. Selenide (1.5 microM) showed a strong inhibitory effect on the enzyme activity of 5LO. In EPR, selenide abolished the signal at g = 6.2, typical for enzymatically active 5LO. Lipid hydroperoxide added to selenide-treated 5LO could not reinstate the signal at g = 6.2, indicating an irreversible change of the coordination of the active site iron.

Arachidonate 5-Lipoxygenase↗

PubMed2001

Combinations of protein-disulfide isomerase domains show that there is little correlation between isomerase activity and wild-type growth.

Protein-disulfide isomerase (PDI) has five domains: a, b, b', a' and c, all of which except c have a thioredoxin fold. A single catalytic domain (a or a') is effective in catalyzing oxidation of a reduced protein but not isomerization of disulfides (Darby, N. J., and Creighton, T. E. (1995) Biochemistry 34, 11725-11735). To examine the structural basis for this oxidase and isomerase activity of PDI, shuffled domain mutants were generated using a method that should be generally applicable to multidomain proteins. Domains a and a' along with constructs ab, aa', aba', ab'a' display low disulfide isomerase activity, but all show significant reactivity with mammalian thioredoxin reductase, suggesting that the structure is not seriously compromised. The only domain order that retains significant isomerase activity has the b' domain coupled to the N terminus of the a' domain. This b'a'c has 38% of the isomerase activity of wild-type PDI, equivalent to the activity of full-length PDI with one of the active sites inactivated by mutation (Walker, K. W., Lyles, M. M., and Gilbert, H. F. (1996) Biochemistry 35, 1972-1980). Individual a and a' domains, despite their very low isomerase activities in vitro, support wild-type growth of a pdi1Delta Saccharomyces cerevisiae strain yeast. Thus, most of the PDI structure is dispensable for its essential function in yeast, and high-level isomerase activity appears not required for viability or rapid growth.

Binding Sites↗

PubMed2001

Up-regulation of thioredoxin and thioredoxin reductase in human malignant pleural mesothelioma.

Thioredoxin (Trx) with a redoxactive dithiol together with NADPH and thioredoxin reductase (TrxR) is a major disulfide reductase regulating cellular redox state and cell proliferation and possibly contributing to the drug resistance of malignant cells. We assessed the Trx system in malignant pleural mesothelioma cell lines, in nonmalignant pleural mesothelium and in biopsies of malignant pleural mesothelioma. The mRNA and immunoreactive proteins of Trx and cytosolic and mitochondrial TrxR were positive in all four human mesothelioma cell lines investigated. Six cases of nonmalignant, histologically healthy pleural mesothelium showed no Trx or TrxR immunoreactivity, whereas immunohistochemistry on 26 biopsies of human malignant pleural mesothelioma showed positive Trx in all cases and positive TrxR in 23 (88%) of the cases. Moderate or strong immunoreactivity for Trx or TrxR was detected in 85% (22 cases) and 61% (14 cases) of the mesothelioma cases, respectively. Both Trx and TrxR staining patterns were mainly diffuse and cytoplasmic, but in 39% of the mesothelioma cases prominent nuclear staining could also be detected. Although staining for Trx and TrxR was seen in tumor cells, no significant association could be demonstrated between Trx or TrxR expression and tumor cell proliferation or apoptosis in the biopsies of mesothelioma. There was no significant association between the intensity of Trx or TrxR immunoreactivity and patient survival, which may possibly be related to moderate or intense Trx and TrxR reactivity in most of the cases. Although the Trx system may have an important role in the drug resistance of malignant mesothelioma, these studies also suggest that multiple factors contribute to the promotion, cell proliferation and apoptosis of malignant mesothelioma cells in vivo.

Adult↗

PubMed2001

Truncated thioredoxin (Trx80) induces production of interleukin-12 and enhances CD14 expression in human monocytes.

Human thioredoxin (Trx) is the major 12-kd cellular disulfide-reductase that on secretion acts as a cocytokine with several interleukins. Truncated Trx with the 80 N-terminal residues (Trx80), also present in plasma, was by itself a mitogenic cytokine for human peripheral blood mononuclear cells (PBMC). This study investigated which cells in PBMC are targets of recombinant Trx80. Purified human CD14(+) monocytes, but not B or T cells, in a synthetic medium were activated to differentiation by Trx80 as measured by flow cytometry of surface antigens because exposure to 100 nM Trx80 increased expression of CD14, CD40, CD54, and CD86. Proliferation of the monocytes was increased in a dose-dependent manner by Trx80 in concentrations ranging from 10 nM to 1 microM. Trx or interleukin (IL) 2 did not induce proliferation or expression of surface antigens on monocytes. Trx80 alone induced secretion of IL-12 from CD40(+) monocytes in the PBMC cultures and this effect was enhanced by IL-2. Trx80 and IL-2 together were strongly synergistic to induce secretion of interferon-gamma in PBMC cultures. The results showed that Trx80 is a potent cytokine for normal human monocytes and directs the immune system in favor of a Th1 response via IL-12 production.

Antigens, CD↗

PubMed2001

Fluorescently labeled model DNA sequences for exonucleolytic sequencing.

We describe here the enzyme-catalyzed, low-density labeling of DNAs with fluorescent dyes. Firstly, for "natural" template DNAs, dNTPs were partially substituted in the labeling reactions by the respective fluorophore-bearing analogs. The DNAs were labeled by PCR using Taq DNA polymerase. The covalent incorporation of dye-dNTPs decreased in the following order: rhodamine-green-5-dUTP (Molecular Probes, the Netherlands), tetramethylrhodamine-4-dUTP (FluoroRed, Amersham Pharmacia Biotech), Cy5-dCTP (Amersham Pharmacia Biotech). Exonucleolytic degradation by the 3'-->5' exonuclease activity of T7 DNA polymerase (wild type) in the presence of excess reduced thioredoxin proceeded to complete breakdown of the labeled DNAs. The catalytic cleavage constants determined by fluorescence correlation spectroscopy were between 0.5 and 1.5 s(-1) at 16 degrees C, normalized for the covalently incorporated dye-nucleotides. Secondly, rhodamine-green-X-dUTP (Roche Diagnostics), tetramethylrhodamine-6-dUTP (Roche Diagnostics), and Cy5-dCTP were covalently incorporated into the antisense strand of "synthetic" 218-b DNA template constructs (master sequences) at well defined positions, starting from the primer binding site, by total substitution for the naturally occurring dNTPs. The 218-b DNA constructs were labeled by PCR with a thermostable 3'-->5' exonuclease deficient mutant of the Tgo DNA polymerase which we have selected. The advantage of the special, synthetic DNA constructs as compared to natural DNAs lies in the possibility of obtaining tailor-made nucleic acids, optimized for testing the performance of exonucleolytic sequencing. The number of incorporated fluorescent nucleotides determined by complete exonucleolytic degradation and fluorescence correlation spectroscopy were six out of six possible incorporations for rhodamine-green-X-dUTP and tetramethylrhodamine-6-dUTP, respectively. Their covalent and base-specific incorporations were confirmed by the novel analysis methodology of re-sequencing (i.e. mobility-shift gel electrophoresis, reversion-PCR and re-sequencing) first developed in the paper Földes-Papp et al. (2001) and in this paper. This methodology was then used by other groups within the whole sequencing project.

Base Sequence↗