Tandem DNA Research Articles

A ranking index for quality assessment of forensic DNA profiles

BackgroundAssessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights) of the capillary electrophoresis electropherograms.ResultsWe recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI) (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009) 951-958). FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles.ConclusionsThe developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification.

A Non-Coding RNA Within the Rasgrf1 Locus in Mouse Is Imprinted and Regulated by Its Homologous Chromosome in Trans

Background Rasgrf1 is imprinted in mouse, displaying paternal allele specific expression in neonatal brain. Paternal expression is accompanied by paternal-specific DNA methylation at a differentially methylated domain (DMD) within the locus. The cis-acting elements necessary for Rasgrf1 imprinting are known. A series of tandem DNA repeats control methylation of the adjacent DMD, which is a methylation sensitive enhancer-blocking element. These two sequences constitute a binary switch that controls imprinting and represents the Imprinting Control Region (ICR). One paternally transmitted mutation, which helped define the ICR, induced paramutation, in trans, on the maternal allele. Like many imprinted genes, Rasgrf1 lies within an imprinted cluster. One of four noncoding transcripts in the cluster, AK015891, is known to be imprinted.Methodology/Principal FindingsHere we demonstrate that an additional noncoding RNA, AK029869, is imprinted and paternally expressed in brain throughout development. Intriguingly, any of several maternally inherited ICR mutations affected expression of the paternal AK029869 transcript in trans. Furthermore, we found that the ICR mutations exert different trans effects on AK029869 at different developmental times.Conclusions/SignificanceFew trans effects have been defined in mammals and, those that exist, do not show the great variation seen at the Rasgrf1 imprinted domain, either in terms of the large number of mutations that produce the effects or the range of phenotypes that emerge when they are seen. These results suggest that trans regulation of gene expression may be more common than originally appreciated and that where trans regulation occurs it can change dynamically during development.

Molecular diagnosis of gestational trophoblastic disease

Gestational trophoblastic disease consists of well-defined diagnostic entities of proliferative disorder of the placenta, of which hydatidiform moles are common lesions. Even with available ancillary studies, including ploidy and immunohistochemistry analyses, histological diagnosis of molar pregnancies can be challenging in a significant percentage of the cases. Reliable diagnostic approaches with improved sensitivity and specificity are highly desirable. Recently, PCR-based short tandem repeat DNA genotyping has emerged as a powerful diagnostic measure in the workup of gestational trophoblastic disorders, particularly hydatidiform moles.

Characterization of the Yeast Telomere Nucleoprotein Core: Rap1 BINDS INDEPENDENTLY TO EACH RECOGNITION SITE

At the core of Saccharomyces cerevisiae telomeres is an array of tandem telomeric DNA repeats bound site-specifically by multiple Rap1 molecules. There, Rap1 orchestrates the binding of additional telomere-associated proteins and negatively regulates both telomere fusion and length homeostasis. Using electron microscopy, viscosity, and light scattering measurements, we show that purified Rap1 is a monomer in solution that adopts a ringlike or C shape with a central cavity. Rap1 could orchestrate telomere function by binding multiple telomere array sites through either cooperative or independent mechanisms. To determine the mechanism, we analyze the distribution of Rap1 monomers on defined telomeric DNA arrays. This analysis clearly indicates that Rap1 binds independently to each nonoverlapping site in an array, regardless of the spacing between sites, the total number of sites, the affinity of the sites for Rap1, and over a large concentration range. Previous experiments have not clearly separated the effects of affinity from repeat spacing on telomere function. We clarify these results by testing in vivo the function of defined telomere arrays containing the same Rap1 binding site separated by spacings that were previously defined as low or high activity. We find that Rap1 binding affinity in vitro correlates with the ability of telomeric repeat arrays to regulate telomere length in vivo. We suggest that Rap1 binding to multiple sites in a telomere array does not, by itself, promote formation of a more energetically stabile complex.

Effects of Preexercise Feeding on Markers of Satellite Cell Activation

The purpose of this study was to determine if consuming isoenergetic (25 g) doses of carbohydrate or protein versus a noncaloric placebo before conventional resistance training affected the myogenic expression of cell cycle-regulating genes as well as the muscle [DNA] acutely after exercise. Ten untrained men (mean +/- SD: age = 22 +/- 4 yr, body mass = 77.8 +/- 8.3 kg, percent body fat = 17.8 +/- 4.0) participated in three resistance exercise sessions (three sets of 10 repetitions at 80% one-repetition maximum for the bilateral hack squat, leg press, and leg extension exercises) in a crossover fashion, which were preceded by carbohydrate, protein, or placebo ingestion 30 min before training. Presupplement/preexercise and 2- and 6-h postexercise muscle biopsies were obtained during each session and analyzed for fold changes in CDK4, CYCLIN D1, MGF, MYOD, P21(CIP1), and P27(KIP1) messenger RNA expression using real-time reverse transcriptase-polymerase chain reaction as well as muscle [DNA] using cuvette-based fluorometric methods. Nonparametric statistics were completed, and no conditions x time interaction effects were revealed. Several exercise-mediated responses were found to occur independent of condition: 1) muscle [DNA] increased at 6 h (+40%, P < 0.05), 2) CDK4 expression increased at 6 h (+86%, P < 0.05), 3) MYOD expression increased at 6 h (+98%, P < 0.05), 4) P27(KIP1) expression decreased at 2 h (j35%, P < 0.05) and 6 h (-59%, P < 0.001), and 5) P21(CIP1) expression substantially increased 2 and 6 h postexercise (+1.250% and +4.670%, respectively, P < 0.001). The tandem DNA and cell cycle regulator gene expression analyses provide preliminary evidence to suggest that satellite cell activation and proliferation may be occurring at early post-exercise time points after a conventional resistance exercise bout, a phenomenon that may seemingly be independent of preexercise macronutrient ingestion.

Detailed Molecular Fingerprinting of Four New Anaplastic Thyroid Carcinoma Cell Lines and Their Use for Verification of RhoB as a Molecular Therapeutic Target

Anaplastic thyroid carcinoma (ATC) is a highly aggressive carcinoma in need of therapeutic options. One critical component of drug discovery is the availability of well-characterized cell lines for identification of molecular mechanisms related to tumor biology and drug responsiveness. Up to 42% of human thyroid cancer cell lines are redundant or not of correct tissue origin, and a comprehensive analysis is currently nonexistent. Mechanistically, RhoB has been identified as a novel molecular target for ATC therapy. The aim was to develop four ATC cell lines detailing genetic, molecular, and phenotypic characteristics and to test five classes of drugs on the cell lines to determine whether they inhibited cell proliferation in a RhoB-dependent fashion. Four cell lines were derived from ATC tumors. Short tandem DNA repeat and mutational status of the originating tumors and cell lines were performed along with molecular and phenotypic characterizations. Compounds were tested for growth inhibition and ability to up-regulate RhoB. Cell line authenticity was confirmed by DNA short tandem repeat analysis. Each proved unique regarding expression of thyroid markers, oncogene status, amplified and deleted genes, and proliferative growth rates. FTI-277, GGTI-286, lovastatin, romidepsin, and UCN-01 up-regulated RhoB and inhibited cell proliferation in a dose-responsive fashion with only romidepsin and FTI-277 being RhoB dependent. Molecular descriptions of thyroid lines were matched to the originating tumors, setting a new standard for cell line characterization. Furthermore, suppressed RhoB is implicated as a molecular target for therapy against ATC because five classes of drugs up-regulate RhoB and inhibit growth dose-responsively.

Integrated Microfluidic System for Rapid Forensic DNA Analysis: Sample Collection to DNA Profile

We demonstrate a conduit for the delivery of a step change in the DNA analysis process: A fully integrated instrument for the analysis of multiplex short tandem repeat DNA profiles from reference buccal samples is described and is suitable for the processing of such samples within a forensic environment such as a police custody suite or booking office. The instrument is loaded with a DNA processing cartridge which incorporates on-board pumps and valves which direct the delivery of sample and reagents to the various reaction chambers to allow DNA purification, amplification of the DNA by PCR, and collection of the amplified product for delivery to an integral CE chip. The fluorescently labeled product is separated using micro capillary electrophoresis with a resolution of 1.2 base pairs (bp) allowing laser induced fluorescence-based detection of the amplified short tandem repeat fragments and subsequent analysis of data to produce a DNA profile which is compatible with the data format of the UK DNA database. The entire process from taking the sample from a suspect, to database compatible DNA profile production can currently be achieved in less than 4 h. By integrating such an instrument and microfluidic cartridge with the forensic process, we believe it will be possible in the near future to process a DNA sample taken from an individual in police custody and compare the profile with the DNA profiles held on a DNA Database in as little as 3 h.

The Terminal Telomeric DNA Sequence Determines the Mechanism of Dysfunctional Telomere Fusion

Mammalian telomeres consist of tandem DNA repeats that bind protective protein factors collectively termed shelterins. Telomere disruption typically results in genome instability induced by telomere fusions. The mechanism of telomere fusion varies depending on the means of telomere disruption. Here, we investigate telomere fusions caused by overexpression of mutant telomerases that add mutated telomeric repeats, thereby compromising shelterin binding to telomeric termini. While all mutant telomeric sequences tested induced heterodicentric chromosome fusions in ATM-competent cells, only those mutant repeat sequences with significant self complementarity induced ATM-independent sister chromatid and isodicentric chromosome fusions. Thus, once a telomere becomes dysfunctional, the terminal telomeric sequence itself determines the fate of that telomere. These results suggest that annealing of self-complementary DNA sequence engages an alternative telomere fusion pathway in human cells, and provide one explanation for the conspicuous lack of self complementarity in the majority of known naturally occurring eukaryotic telomeric sequences.

Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex.

The Central glycolytic genes Repressor (CggR) from Bacillus subtilis belongs to the SorC family of transcription factors that control major carbohydrate metabolic pathways. Recent studies have shown that CggR binds as a tetramer to its tandem operator DNA sequences and that the inducer metabolite, fructose 1,6-bisphosphate (FBP), reduces the binding cooperativity of the CggR/DNA complex. Here, we have determined the effect of FBP on the size, shape and stoichiometry of CggR complexes with full-length and half-site operator sequence by small-angle X-ray scattering, size-exclusion chromatography, fluorescence cross-correlation spectroscopy and noncovalent mass spectrometry (MS). Our results show that CggR forms a compact tetrameric assembly upon binding to either the full-length operator or two half-site DNAs and that FBP triggers a tetramer–dimer transition that leaves a single dimer on the half-site or two physically independent dimers on the full-length target. Although the binding of other phospho-sugars was evidenced by MS, only FBP was found to completely disrupt dimer–dimer contacts. We conclude that inducer-dependent dimer–dimer bridging interactions constitute the physical basis for CggR cooperative binding to DNA and the underlying repression mechanism. This work provides experimental evidences for a cooperativity-based regulation model that should apply to other SorC family members.

Development and Evaluation of a Sensitive PCR-ELISA System for Detection of Schistosoma Infection in Feces

BackgroundA PCR-enzyme-linked immunosorbent assay (PCR-ELISA) was developed to overcome the need for sensitive techniques for the efficient diagnosis of Schistosoma infection in endemic settings with low parasitic burden.Methodology/Principal FindingsThis system amplifies a 121-base pair tandem repeat DNA sequence, immobilizes the resultant 5′ biotinylated product on streptavidin-coated strip-well microplates and uses anti-fluorescein antibodies conjugated to horseradish peroxidase to detect the hybridized fluorescein-labeled oligonucleotide probe. The detection limit of the Schistosoma PCR-ELISA system was determined to be 1.3 fg of S. mansoni genomic DNA (less than the amount found in a single cell) and estimated to be 0.15 S. mansoni eggs per gram of feces (fractions of an egg). The system showed good precision and genus specificity since the DNA target was found in seven Schistosoma DNA samples: S. mansoni, S. haematobium, S. bovis, S. intercalatum, S. japonicum, S. magrebowiei and S. rhodaini. By evaluating 206 patients living in an endemic area in Brazil, the prevalence of S. mansoni infection was determined to be 18% by examining 12 Kato-Katz slides (41.7 mg/smear, 500 mg total) of a single fecal sample from each person, while the Schistosoma PCR-ELISA identified a 30% rate of infection using 500-mg of the same fecal sample. When considering the Kato-Katz method as the reference test, artificial sensitivity and specificity rates of the PCR-ELISA system were 97.4% and 85.1%, respectively. The potential for estimating parasitic load by DNA detection in feces was assessed by comparing absorbance values and eggs per gram of feces, with a Spearman correlation coefficient of 0.700 (P<0.0001).Conclusions/SignificanceThis study reports the development and field evaluation of a sensitive Schistosoma PCR-ELISA, a system that may serve as an alternative for diagnosing Schistosoma infection.

Induction of antigen-specific CTL and antibody responses in mice by a novel recombinant tandem repeat DNA vaccine targeting at mucin 1 of pancreatic cancer

Tandem repeat (TR) is the key epitope of mucin 1 (MUC1) for inducing cytotoxic T lymphocytes (CTL) to kill the tumor cells specifically. This study aimed to construct a new recombinant DNA vaccine based on single TR and to investigate the induced immune responses in mice. After the synthesis of a recombinant human TR(rhTR)and the construction of the recombinant plasmid pcDNA3.1-TR/Myc-his (+) A (pTR plasmid), C57BL/6 (H-2(b)) mice were immunized with it (TR group, n = 15). Mice inoculated with the empty vector (EV group, n = 15) and normal saline (NS group, n = 15) were used as vector and blank control, respectively. Cytotoxic assay was carried out to measure the CTL activity. And indirect enzyme-linked immunosorbent assay (ELISA) was used to detect anti-TR-specific antibodies. TR group resulted in more efficient induction of CTL-specific cytolysis against TR polypeptide than both EV and NS groups (both P < 0.01). Vaccine-immunized mice had a higher equivalent concentration of anti-TR-specific antibodies (2,324 ± 238 μg/ml) than either of EV group (1,896 ± 533 μg/ml, P < 0.01) or NS group (1,736 ± 142 μg/ml, P < 0.01). The novel recombinant TR DNA vaccine targeting at MUC1 of pancreatic cancer was constructed successfully, effectively expressing TR polypeptide in the transfected mammalian cells and inducing TR-specific CTL and antibody response.

Sensitive and simple detection of Escherichia coli strain based on time-resolved fluorescence DNA hybridization assay

A two-probe tandem DNA hybridization assay based on time-resolved fluorescence was employed to detect Escherichia coli strain. The amino modified capture probe was covalently immobilized on the common glass slide surface. The Eu(TTA) 3(5-NH 2-phen) with the characteristics of long lifetime and intense luminescence was labeled with reporter probe. The original extracted DNA samples without the purification and amplification process were directly used in the hybridization assay. The concentration of capture probe, hybridization temperature, hybridization and washing time were optimized. The detection limit is about 1.49 × 10 3 CFU mL −1 E. coli cells, which is comparable to the value of most microbiology methods. The proposed method has the advantages of easy operation, satisfactory sensitivity and specificity, which can provide a promising technique for monitoring the microorganisms.

KpnI-repetitive DNA element tandemly clustered on subtelomeric regions of Triticeae genome

A new class of tandem repetitive DNA element was identified from Triticeae genome. A genomic DNA library was constructed from Aegilops tauschii by cleavage with KpnI. The novel repetitive sequence p...

The Judicial Use of DNA Evidence and Forensic Expert Testimony in the Criminal Justice System

In the forensic sciences, DNA analysis is especially useful in sexual assault cases where body contact is made or bodily fluids are exchanged. However, its usefulness can be severely limited within the contour of the criminal justice system. This article discusses a case wherein short tandem repeat DNA typing was used to charge the defendant with sexual assault of a child. The State’s DNA technicians analyzed the victim’s underclothing and reviewed the victim’s sexual assault nurse examination (SANE). Our independent review of the State’s forensic laboratory work showed that the samples used to obtain a DNA match from the victim’s underclothing and the defendant revealed a third contributor. An allele was found that did not match either the victim or the defendant as shown by us as expert witness. A ruling by the trial judge limited what the jury was allowed to hear regarding our findings. The defendant was found guilty. The defendant appealed the guilty verdict based on the trial judge’s decision to limit defense expert witness testimony. Following established law, the appellate court upheld the conviction, ruling that a victim’s testimony alone, with or without any corroborating forensic evidence, supports a finding of guilt.

Integration of growth hormone gene constructs in transgenic strains of coho salmon (Oncorhynchus kisutch) at centromeric or telomeric sites

Very little information is currently available regarding the sites of integration of transgenes in genetically engineered fish. We examined the chromosomal location of growth hormone gene constructs containing GH1 in three different strains of transgenic coho salmon produced by microinjection into pronuclei of fertilized eggs. The constructs were labeled and used as probes in fluorescence in situ hybridization experiments on chromosome preparations from the M77, MT5750A, and H3D0474 strains of transgenic coho salmon. The constructs were localized at 1-3 different sites in different strains. In the M77 strain the construct was found at a single centromeric site on a medium-sized metacentric chromosome, while in the MT5750A strain, the construct was found at a single telomeric site on the short arm of chromosome pair 21, a subtelocentric chromosome with a large band of repetitive DNA on the short arm. In the H3D0474 strain, the construct was found at telomeric sites on the long arms of three metacentric chromosomes that appear to represent one pair of homologous chromosomes and one chromosome containing the homeologous long arm (recently duplicated chromosome arm) corresponding to the long arm of the first pair. This suggests transfer of the construct may have occurred by homologous and homeologous crossing over. All of the constructs incorporated at restricted sites characterized by the presence of tandem DNA repeats.

A novel bifunctional europium complex as a potential fluorescent label for DNA detection

A bifunctional europium complex of Eu(TTA)(3)(5-NH(2)-phen) using 2-thenoyltrifluoroacetonate (TTA) and 5-amino-1,10-phenanthroline (5-NH(2)-phen) as ligand reagents was applied in DNA detection assays for the first time. The complex has a long fluorescence lifetime, high fluorescence quantum yield, and is easy to label oligonucleotides for time-resolved fluorescence bioanalysis. A two-probe tandem DNA hybridization assay including capture DNA(1), probe DNA(2), and target DNA(3) was employed to detect microbial pathogens. The DNA sequences in the assay were designed using software Primer Premier 5.0 based on published specific nucleotide sequences of Staphylococcus aureus and Escherichia coli. 3'-Amino-modified capture DNA(1) was covalently immobilized on the common glass slide surface and the 5'-amino-modified probe DNA(2) was combined with the functionalized Eu(TTA)(3)(5-NH(2)-phen) via glutaraldehyde. The detection was done by monitoring the fluorescence intensity from the glass surface after the hybridization reaction with complementary target DNA(3). The optimal concentration of capture DNA(1) of 1.0 x 10(-6) mol l(-1) dropped onto the glass slides and optimal hybridization temperatures of 48 degrees C and 39 degrees C respectively for Staphylococcus aureus and Escherichia coli were obtained. The proposed DNA detection system showed higher sensitivity than such a complex doped nanoparticle-based detection system in our previous study for the better uniformity and dispersity of monomolecular labels. The sensing system presented a short hybridization time of 2 h, satisfactory stability, and high selectivity. The results demonstrate that this complex might be a potentially excellent dye in area of biochemical analysis.

Abstract B64: Telomeric DNA sequence determines the mechanism of dysfunctional telomere fusion in human cancer cells

Abstract Cancer cells rely on the ribonucleoprotein enzyme telomerase to maintain their telomeres, which consist of tandem DNA repeats bound to protective protein factors collectively termed shelterin. Experimentally-induced telomere dysfunction in cancer cells, either through critical telomere shortening or disruption of shelterin binding, typically leads to telomere fusions, ultimately resulting in genome instability and cell death. For reasons that are not well understood, the mechanism of telomere fusion varies depending on the cause of telomere dysfunction. We have investigated telomere fusions caused by overexpression of mutant telomerases that add mutated telomeric repeats, thereby disrupting shelterin binding and inhibiting cancer cell proliferation. We previously showed that the effect of one such telomerase in human cancer cells is ATM dependent (Stohr BA and Blackburn EH, Cancer Research 68:5309–5317, 2008). Here, we have tested additional mutant telomerases that add either palindromic or non-palindromic telomeric repeats. We show that while all mutant telomeric sequences tested induce heterodicentric chromosome fusions, only palindromic telomeric repeats induce ATM-independent sister chromatid and isodicentric chromosome fusions in human cancer cells. Thus, the telomeric sequence itself influences the fate of telomeres that have become dysfunctional. These results implicate DNA strand annealing in an alternative telomere fusion pathway in human cells. The need to avoid genome instability caused by such fusions is one explanation for the characteristic lack of self-complementarity in naturally-occurring telomeric sequences. Finally, our results have significant implications for the translational application of mutant telomerases as a cancer therapeutic strategy. Citation Information: Cancer Res 2009;69(23 Suppl):B64.

Generation of genetic diversity in microsporidia via sexual reproduction and horizontal gene transfer

Microsporidia are obligate intracellular pathogens mainly infecting both vertebrate and invertebrate hosts. The group comprises approximately 150 genera with 1,200 species. Due to sequence divergence phylogenic reconstructions that are solely based on DNA sequence have been unprecise for these pathogens. Our previous study identified that three microsporidian genomes contained a putative sex-related locus similar to that of zygomycetes. In a comparison of genome architecture of the microsporidia to other fungi, Rhizopus oryzae, a zygomycete fungus, shared more common gene clusters with Encephalitozoon cuniculi, a microsporidian. This provides evidence supporting the hypothesis that microsporidia and zygomycete fungi may share a more recent common ancestor than other fungal lineages. Genetic recombination is an important outcome of sexual development. We describe genetic markers which will enable tests of whether sex occurs within E. cuniculi populations by analyzing tandem repeat DNA regions in three different isolates. Taken together, the phylogenetic relationship of microsporidia to fungi and the presence of a sex-related locus in their genomes suggest the microsporidia may have an extant sexual cycle. In addition, we describe recently reported evidence of horizontal gene transfer from Chlamydia to the E. cuniculi genome and show that these two obligate intracellular pathogens can infect the same host cells.

Comparison of two genetically related Entamoeba histolytica cell lines derived from the same isolate with different pathogenic properties

Entamoeba histolytica is known for its extraordinary capacity to destroy human tissues, leading to invasive diseases such as ulcerative colitis or extra-intestinal abscesses. In order to identify the virulence factors of this parasite phenotypes and proteomes of two recently identified genetically related cell lines (A and B), derived from the laboratory E. histolytica isolate HM-1:IMSS, were compared. Both cell lines are indistinguishable on the basis of highly polymorphic tandem repeat DNA sequences. However, cell line A is incapable to induce liver abscesses in experimentally infected rodents, whereas cell line B provokes considerable abscesses. Phenotypic analyses revealed increased hemolytic activity, lower growth rate, smaller cell size, reduced cysteine peptidase activity and lower resistance to nitric oxide stress for cell line A. In contrast, no differences between the two cell lines were found for cytopathic activity, erythrophagocytosis, digestion of erythrocytes or resistance to complement, hydrogen peroxide and superoxide radical anions. Proteomic comparison by 2-D DIGE followed by MS, identified a total of 21 proteins with higher abundance in cell line A and ten proteins with higher abundance in cell line B. Remarkably, three differentially up-regulated antioxidants were exclusively found in the pathogenic cell line B. Notably, only for two differentially regulated proteins, namely a Fe-hydrogenase and a C2 domain protein, a similar type was found at the level of transcription. Summarized, a defined set of different proteins could be identified between cell lines A and B. These molecules may have an important role in amoeba pathogenicity.

Time-resolved fluorescence based DNA detection using novel europium ternary complex doped silica nanoparticles

A two-probe tandem DNA hybridization assay including capture DNA 1, probe DNA 2, and target DNA 3 was prepared. The long-lived luminescent europium complex doped nanoparticles (NPs) were used as the biomarker. The complex included in the particle was Eu(TTA) 3(5-NH 2-phen)-IgG (ETN-IgG), the europium complex Eu(TTA) 3(5-NH 2-phen) linking an IgG molecule. Silica NPs containing ETN-IgG were prepared by the reverse microemulsion method, and were easy to label oligonucleotide for time-resolved fluorescence assays. The luminophores were well-protected from the environmental interference when they were doped inside the silica network. The sequences of Staphylococcus aureus and Escherichia coli genes were designed using software Primer Premier 5.0. Amino-modified capture DNA 1 was covalently immobilized on the common glass slides surface. The detection was done by monitoring the fluorescence intensity from the glass surface after the hybridization reaction with the NPs labeled probe DNA 2 and complementary target DNA 3. The sensing system presented short hybridization time, satisfactory stability, sensitivity, and selectivity. This approach was successfully employed for preliminary application in the detection of pure cultured E. coli, it might be an effective tool for pathogen DNA monitoring.