Target DNA Molecules Research Articles

Electrostatic Detection of Unlabelled Single- and Double-stranded DNA Using Capacitive Field-effect Devices Functionalized with a Positively Charged Polyelectrolyte Layer

Capacitive field-effect electrolyte-insulator-semiconductor sensors consisting of an Al-p-Si-SiO2 structure have been used for the electrical detection of unlabelled single- and double-stranded DNA (dsDNA) molecules by their intrinsic charge. A simple functionalization protocol based on the layer-by-layer (LbL) technique was used to prepare a weak polyelectrolyte/probe-DNA bilayer, followed by the hybridization with complementary target DNA molecules. Due to the flat orientation of the LbL-adsorbed DNA molecules, a high sensor signal has been achieved. In addition, direct label-free detection of in-solution hybridized dsDNA molecules has been studied.

Microfluidics-based in situ padlock/rolling circle amplification system for counting single DNA molecules in a cell.

In situ padlock/rolling circle amplification (RCA) is a method used to amplify, visualize, and quantify target DNA molecules in cells. However, the multiple reaction steps involved make this technique costly and cumbersome. We developed a novel, simplified, automated microfluidic system for RCA, and demonstrated its effectiveness by counting amplified mitochondrial DNA fragments in HeLa cells. After optimizing the volume of the reaction solutions and washing buffer composition, the product yield was equal to that obtained by the conventional manual method. The required volume of reagents was reduced to 10 μL, which is less than half the volume used in the conventional method. To the best of our knowledge, this is the first report of an automated microfluidic method for in situ padlock/RCA, which can be useful for making highly efficient pathological diagnoses.

Real-time PCR-based identification of bacterial and fungal pathogens from blood samples.

Latest major contributions in the field of sepsis diagnostics result from advances in PCR technologies permitting new standards in speed and quality, given the fact that a timely diagnosis is the decisive factor to the survival of patients with bloodstream infections.Multiplex real-time PCR is a quantitative method for simultaneous amplification and detection of different targeted DNA molecules within hours. Nevertheless, various studies have shown a number of technical shortcomings as well as a high heterogeneity in sensitivity.The present method allows the standardized and rapid detection and identification of 25 common bacteria and fungi responsible for bloodstream infections from whole blood samples by using LightCycler(®) SeptiFast (LC-SF) test, based on real-time PCR.

In situ synthesis of peptide nucleic acids in porous silicon for drug delivery and biosensing.

Peptide nucleic acids (PNA) are a unique class of synthetic molecules that have a peptide backbone and can hybridize with nucleic acids. Here, a versatile method has been developed for the automated, in situ synthesis of PNA from a porous silicon (PSi) substrate for applications in gene therapy and biosensing. Nondestructive optical measurements were performed to monitor single base additions of PNA initiated from (3-aminopropyl)triethoxysilane attached to the surface of PSi films, and mass spectrometry was conducted to verify synthesis of the desired sequence. Comparison of in situ synthesis to postsynthesis surface conjugation of the full PNA molecules showed that surface mediated, in situ PNA synthesis increased loading 8-fold. For therapeutic proof-of-concept, controlled PNA release from PSi films was characterized in phosphate buffered saline, and PSi nanoparticles fabricated from PSi films containing in situ grown PNA complementary to micro-RNA (miR) 122 generated significant anti-miR activity in a Huh7 psiCHECK-miR122 cell line. The applicability of this platform for biosensing was also demonstrated using optical measurements that indicated selective hybridization of complementary DNA target molecules to PNA synthesized in situ on PSi films. These collective data confirm that we have established a novel PNA–PSi platform with broad utility in drug delivery and biosensing.

Fast on-site diagnosis of influenza A virus by Palm PCR and portable capillary electrophoresis.

A method combining Palm polymerase chain reaction (PCR) and portable capillary electrophoresis (CE) was developed for rapid on-site analysis of influenza A (H1N1) virus. The portable CE system was suitable for rapid diagnosis which was able to detect a sample in ∼4 min after sample loading, while the 'Palm PCR' system allowed for high-speed nucleic acid amplification in ∼16 min. The analysis time from DNA sample to analysis of amplified target DNA molecule was only ∼20 min, which was significantly less than slab gel electrophoresis with other commercially available PCR machine. When the 100-bp DNA ladder was separated, the relative standard deviation values (n=5) for the migration times and peak areas of the 100 and 200-bp DNA molecules were 0.26 and 8.9%. The detection limits were 6.3 and 7.2 pg/μL, respectively. The combined method was also able to identify two influenza A-associated genes (the HA and NP genes of the novel H1N1 influenza). CE separation was achieved with a sieving matrix of 1% poly(vinylpyrrolidone) (Mr=1,300,000) in 1× TBE buffer (pH 8.45). The combined Palm PCR-portable CE system should provide an improved, fast on-site molecular genetic diagnostic method.

O-0021 - Outcome According to Tumor Ras Mutation Status in Opus Study Patients with Metastatic Colorectal Cancer Randomized to FOLFOX4 with or Without Cetuximab as First-Line Treatment

Introduction: The randomized phase II OPUS study demonstrated that the addition of cetuximab to FOLFOX4 significantly improved response and progression-free survival in the first-line treatment of patients with KRAS codon 12/13 (hereinafter, exon 2) wild-type metastatic colorectal cancer (mCRC). Patients with KRAS exon 2 tumor mutations showed no such cetuximab benefit, with worse outcome in patients in the FOLFOX4 plus cetuximab arm compared with FOLFOX4 alone arm.Methods: Available KRAS exon 2 wild-type tumors from OPUS study patients were screened for 26 mutations (new RAS) in 4 additional KRAS codons (exons 3 and 4) and 6 NRAS codons (exons 2, 3 and 4) using BEAMing technology, an approach based on polymerase chain reaction (PCR) amplification of single target DNA molecules on individual magnetic beads within an emulsion. Bead-associated PCR products from tumor DNA samples were subsequently typed for the presence of mutant or wild-type sequences using specific fluorescent probes and flow cytometry. Where mutations were detected, this approach allowed for the determination of the ratio of mutant to wild-type RAS DNA molecules in the original tumor DNA sample. As the predictive value of low prevalence RAS mutations in tumors in which the overwhelming majority of cells were wild-type was not clear, and in line with current clinical practice in relation to KRAS exon 2 screening, a 5% diagnostic cutoff was selected for analysis. Treatment outcome was subsequently assessed according to RAS mutation status (RAS wild-type, new RAS mutant and RAS mutant [KRAS exon 2 or new RAS]).Results: Mutation status was evaluable in 118/179 (66%) patients with KRAS exon 2 wild-type tumors. New RAS mutations were detected in 31/118 (26%) patients. In those with RAS wild-type tumors, response was significantly improved by the addition of cetuximab to FOLFOX4 (Table). The treatment effect for those with new RAS tumor mutations could not be definitively assessed due to low patient numbers. In patients with any tumor RAS mutation (KRAS exon 2 or new RAS), no benefit from the addition of cetuximab to FOLFOX4 was seen, with a clear trend for worse outcome.Conclusion: In the first-line setting, patients with mCRC harboring any activating RAS mutation are unlikely to benefit from the addition of cetuximab to FOLFOX4. Restricting the administration of FOLFOX4 plus cetuximab to patients with tumors wild-type at all such loci might help further tailoring of therapy to maximize patient benefit. Introduction: The randomized phase II OPUS study demonstrated that the addition of cetuximab to FOLFOX4 significantly improved response and progression-free survival in the first-line treatment of patients with KRAS codon 12/13 (hereinafter, exon 2) wild-type metastatic colorectal cancer (mCRC). Patients with KRAS exon 2 tumor mutations showed no such cetuximab benefit, with worse outcome in patients in the FOLFOX4 plus cetuximab arm compared with FOLFOX4 alone arm. Methods: Available KRAS exon 2 wild-type tumors from OPUS study patients were screened for 26 mutations (new RAS) in 4 additional KRAS codons (exons 3 and 4) and 6 NRAS codons (exons 2, 3 and 4) using BEAMing technology, an approach based on polymerase chain reaction (PCR) amplification of single target DNA molecules on individual magnetic beads within an emulsion. Bead-associated PCR products from tumor DNA samples were subsequently typed for the presence of mutant or wild-type sequences using specific fluorescent probes and flow cytometry. Where mutations were detected, this approach allowed for the determination of the ratio of mutant to wild-type RAS DNA molecules in the original tumor DNA sample. As the predictive value of low prevalence RAS mutations in tumors in which the overwhelming majority of cells were wild-type was not clear, and in line with current clinical practice in relation to KRAS exon 2 screening, a 5% diagnostic cutoff was selected for analysis. Treatment outcome was subsequently assessed according to RAS mutation status (RAS wild-type, new RAS mutant and RAS mutant [KRAS exon 2 or new RAS]). Results: Mutation status was evaluable in 118/179 (66%) patients with KRAS exon 2 wild-type tumors. New RAS mutations were detected in 31/118 (26%) patients. In those with RAS wild-type tumors, response was significantly improved by the addition of cetuximab to FOLFOX4 (Table). The treatment effect for those with new RAS tumor mutations could not be definitively assessed due to low patient numbers. In patients with any tumor RAS mutation (KRAS exon 2 or new RAS), no benefit from the addition of cetuximab to FOLFOX4 was seen, with a clear trend for worse outcome. Conclusion: In the first-line setting, patients with mCRC harboring any activating RAS mutation are unlikely to benefit from the addition of cetuximab to FOLFOX4. Restricting the administration of FOLFOX4 plus cetuximab to patients with tumors wild-type at all such loci might help further tailoring of therapy to maximize patient benefit.

Quantitative assessment of the ion-beam irradiation induced direct damage of nucleic acid bases through FTIR spectroscopy

Energetic particles exist ubiquitously in nature, and when they hit DNA molecules in organisms, they may induce critical biological effects such as mutation. It is however still a challenge to measure directly and quantitatively the damage imposed by the energetic ions on target DNA molecules. In this work we attempted to employ Fourier transformation infrared (FTIR) spectroscopy to assess the ion-induced direct damage of four nucleic acid bases, namely, thymine (T), cytosine (C), guanine (G), and adenine (A), which are the building blocks of DNA molecules. The samples were prepared as thin films, irradiated by argon ion-beams at raised ion fluences, and in the meantime measured by FTIR spectroscopy for the damage in a quasi-in-situ manner. It was found that the low-energy ion-beam induced radiosensitivity of the four bases shows the sequence G>T>C>A, wherein the possible mechanism was also discussed.

Mathematical modeling of functionalized-microsphere based assays for rapid DNA detection: From sample preparation to results

Functionalized microspheres are frequently used in the detection of biomolecules. A fundamental understanding of the mechanisms involved in enzymatic assays is required to estimate a method's utility. The mathematical methodology is illustrated through a theoretical analysis to assess the performance of a diagnostic method based on the horseradish peroxidase catalyzed reaction to detect pathogens in clinical specimens. The first part of the analysis focuses on the collection of target DNA molecules onto a functionalized fiber in a lysis micro-reactor (LMR). Expressions are derived for hybridization rates that include convective transport. In the next step the fiber is contacted with functionalized chitosan microspheres containing horse radish peroxidase. Chitosan microspheres are conjugated to the fiber with the target DNA acting as a unique tether. The final step is the release of chitosan microspheres in a chromogenic substrate and monitoring absorption changes. The analysis provides estimates of the method sensitivity and processing time and we show that DNA with a concentration as low as 10−4 copies per milliliter can be detected in less than 30min. The modeling methodology presented can readily be extended to similar enzymatic, microsphere-based assays for quantitative purposes and feasibility studies.

Coinfection of Human Herpesviruses 6A (HHV-6A) and HHV-6B as Demonstrated by Novel Digital Droplet PCR Assay

The human herpesviruses HHV-6A and HHV-6B have been associated with various neurologic disorders partly due to the detection of elevated viral DNA levels in patients compared to controls. However the reported frequency of these viruses varies widely, likely reflecting differences in PCR methodologies used for detection. Digital droplet PCR (ddPCR) is a third generation PCR technology that enables the absolute quantification of target DNA molecules. Mounting evidence of the biological differences between HHV-6A and HHV-6B has led to their recent reclassification as separate species. As it is now especially relevant to investigate each virus, our objectives were to first design a multiplex HHV-6A and HHV-6B ddPCR assay and then to investigate the incidence of HHV-6A and HHV-6B coinfection in samples from healthy donors and patients with MS, a disease in which HHV-6 is thought to play a role. In our assessment of healthy donors, we observed a heretofore-underappreciated high frequency of coinfection in PBMC and serum, and found that our assay precisely detects both HHV-6A and HHV-6B chromosomally integrated virus, which has important implications in clinical settings. Interestingly, upon comparing the saliva from MS patients and healthy donors, we detected a significantly elevated frequency of coinfection in MS saliva; increased detection of HHV-6A in MS patients is consistent with other studies suggesting that this viral species (thought to be more neurotropic than HHV-6B) is more prevalent among MS patients compared to healthy donors. As the biology and disease associations between these two viral species differ, identifying and quantifying both species of HHV-6 may provide clinically relevant information, as well as enhance our understanding of the roles of each in health and disease.

Revisiting the TALE repeat

Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33–35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.Electronic supplementary materialThe online version of this article (doi:10.1007/s13238-014-0035-2) contains supplementary material, which is available to authorized users.

Size-fitting effect for hybridization of DNA/mercaptohexanol mixed monolayers on gold.

In this article we proposed a simple hexagonal model for exploring the hybridization of thiol-modified probe DNA self-assembled monolayers (SAMs) on gold with target DNA molecules in solution. The size-fitting coefficient d(c)/d(t) from the model was used to discuss the principle for DNA optimal hybridization, where d(c) was the channel diameter among three adjacent probe DNA molecules on gold and dt was the gyration diameter of the target DNA molecules in solution. Experimentally we investigated the hybridization effect (hybridization efficiency H(E) and hybridization density H(D)) of thiol-modified probe DNA (DNA base amount m = 15, 25 or 35)/mercaptohexanol (MCH) mixed SAMs on gold in 1 M electrolyte solution by chronocoulometry (CC) and electrochemical impedance spectroscopy (EIS). The surface coverage Γ(m) of the probe DNA on gold was adjusted by changing the mixed concentration ratio of probe DNA with MCH (C(DNA)/C(MCH)) in the assembly solution. Results indicated that with the increase of C(DNA)/C(MCH), H(E) decreased gradually; H(D) first increased and then decreased, which arrived at the biggest at C(DNA)/C(MCH) = 1 for all the probe DNA/MCH mixed SAMs (m = 15, 25, 35). The optimal Γ(m) for achieving the biggest H(D) in DNA hybridization decreased with the increase of m from 15 to 35. The experimental conclusions obtained by CC and EIS measurements verified each other. Combining the simple model with our experimental results, we ascertained that d(c)/d(t) decreased with the increase of m, which showed a good linear relationship. These conclusions provided an important reference and guidance for controllably constructing DNA sensors with optimal performance.

Self-aligned colocalization of 3D plasmonic nanogap arrays for ultra-sensitive surface plasmon resonance detection

We report extremely sensitive plasmonic detection that was performed label-free based on the colocalization of target DNA molecules and electromagnetic hot spots excited at 3D nanogap arrays. The colocalization was self-aligned by oblique evaporation of a dielectric mask over the 3D nanopatterns, which creates nanogaps for spatially selective target binding. The feasibility was experimentally confirmed by measuring hybridization of 24-mer single-stranded DNA oligonucleotides on triangular and circular 3D nanogap arrays. We were able to achieve significantly amplified optical signatures that lead to sensitivity enhancement in terms of detectable binding capacity in reference to conventional thin film-based surface plasmon resonance detection on the order of 1fg/mm2.

Molecular beacon based biosensor for the sequence-specific detection of DNA using DNA-capped gold nanoparticles-streptavidin conjugates for signal amplification

We describe a highly sensitive and selective molecular beacon-based electrochemical impedance biosensor for the sequence-specific detection of DNA. DNA-capped conjugates between gold nanoparticles (Au-NPs) and streptavidin are used for signal amplification. The molecular beacon was labeled with a thiol at its 5′ end and with biotin at its 3′ end, and then immobilized on the surface of a bare gold electrode through the formation of Au-S bonds. Initially, the molecular beacon is present in the “closed” state, and this shields the biotin from being approached by streptavidin due to steric hindrance. In the presence of the target DNA, the target DNA molecules hybridize with the loop and cause a conformational change that moves the biotin away from the surface of the electrode. The biotin thereby becomes accessible for the reporter (the DNA-streptavidin capped Au-NPs), and this results in a distinct increase in electron transfer resistance. Under optimal conditions, the increase in resistance is linearly related to the logarithm of the concentration of complementary target DNA in the range from 1.0 fM to 0.1 μM, with a detection limit of 0.35 fM (at an S/N of 3). This biosensor exhibits good selectivity, and acceptable stability and reproducibility.

Naked-eye detection of nucleic acids through rolling circle amplification and magnetic particle mediated aggregation

We are presenting a new method for sequence-specific and naked-eye detection of nucleic acids (NAs) through isothermal amplification and magnetic particle mediated aggregation. A padlock probe was designed to hybridize to specific sequence on target genes followed by ligation and rolling circle amplification (RCA). Magnetic particles (MPs) were then added into RCA products solution. MPs would physically combine with long linear DNA coils (such as products of RCA reaction) and form visible intertwined aggregates, while no aggregate was observed in the absence of high molecular weight NAs (>1kb). As little as 0.62amol (124fM) of target DNA molecules was detected by the naked eye. It was further applied to detect human papillomavirus type 18 gene in genomic DNA isolated from HeLa cells. This assay is sensitive and low-cost with minimal instrumentation, revealing great potential for molecular diagnostics in developing countries and regions with limited settings.

Direct Detection of Bacterial Genomic DNA at Sub-Femtomolar Concentrations Using Single Molecule Arrays

We report a method for the sensitive measurement of genomic DNA based on the direct detection of single molecules of DNA in arrays of femtoliter wells. The method begins by generating short fragments of DNA from large, double-stranded molecules of genomic DNA using either restriction enzymes or sonication. Single-stranded fragments are then generated by melting the duplex, and these fragments are hybridized to complementary biotinylated detection probes and capture probes on paramagnetic beads. The resulting DNA complexes are then labeled with an enzyme (streptavidin-β-galactosidase), and single enzymes associated with these complexes on beads are detected in single molecule arrays (Simoa). DNA concentration is quantified by determining the average number of enzymes per bead via Poisson statistics (digital) or the average bead intensity (analog). The Simoa DNA assay was used to detect genomic DNA purified from S. aureus with an average limit of detection (LOD) of 0.07 fM, or 2100 DNA molecules per 50 μL sample. We used this assay to detect S. aureus spiked into (a) whole blood, with an average LOD of 1100 bacteria per 25 μL sample (0.074 fM), and (b) water from the Charles River, with an LOD of 1300 bacteria per 50 μL sample (0.042 fM). Bacteria were detected in river water without prior purification of DNA. The Simoa DNA assay, which directly detects target DNA molecules without molecular replication, is an attractive alternative to existing sensitive DNA detection technologies that rely on amplification using polymerases, such as the polymerase chain reaction (PCR).

An insight into the hybridization mechanism of hairpin DNA physically immobilized on chemically modified graphenes

There is an emerging interest in developing electrochemical DNA biosensors which rely on label-free protocols for the detection of DNA hybridization and polymorphism. Lately, many of them have been using DNA probes which were physically adsorbed onto different graphene platforms. In these works, the biorecognition event is monitored by electrochemical impedance spectroscopy and the detection mechanism proposed needs verification by orthogonal methods. Here, we aim to provide an insight into the mechanism behind the impedimetric signal change upon the hybridization event on graphene platforms. For this aim, we used an orthogonal electrochemical method, differential pulse voltammetry, to examine the oxidation of guanine on target DNA molecules hybridized with an inosine-substituted hairpin DNA probe. We show that the successful biorecognition event leads to desorption of dsDNA from graphenic surfaces on a wide range of graphenic surfaces, such as graphene oxide, electrochemically reduced graphene oxide and thermally reduced graphene oxide. These results confirm the previous hypothesis based on electrochemical impedance spectroscopy data. In addition, these findings also have a profound impact on the understanding of both the interactions between DNA and graphene platforms and the DNA recognition event on graphene platforms for the construction of biosensors.

DNA sequence analysis with droplet-based microfluidics

Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based assay. Using probes of different sequences, we interrogate a target DNA molecule for polymorphisms. With a larger probe set, additional polymorphisms can be interrogated as well as targets of arbitrary sequence.

Ligase chain reaction coupled with rolling circle amplification for high sensitivity detection of single nucleotide polymorphisms

We present a highly sensitive and homogeneous assay for the detection of single nucleotide polymorphisms (SNPs) by ligase chain reaction (LCR) coupled with rolling circle amplification (RCA). The LCR probes include one pair of probes and a padlock probe (PLP). In the LCR, one pair of probes composed of X and Y, perfectly hybridize with the upper strand of the target DNA after thermal denaturation. They are then ligated by the thermostable ligase to form the ligation product of XY. At the same time, the PLP hybridizes with the lower strand of the target DNA and are ligated to form the circular PLP (cPLP). After repeated cycles of denaturation, annealing, and ligation, the target DNA is amplified exponentially to generate a large number of XY and cPLPs. Subsequently, RCA is triggered by the cPLP as a template and XY as a primer, producing large numbers of long strand DNA products, which are detected by binding with the fluorescent dye, SYBR Green I, in a homogeneous manner. This method is simple, and avoids the need for detection of the LCR products with labeled probes and complex separation steps. The assay is sensitive and specific enough to detect a 1 fM target DNA molecule. It is possible to accurately determine the allele frequency as low as 1.0%. The LCR coupled with RCA assay extends the application of the LCR and RCA, and provides a new strategy for detecting SNPs as well as nucleic acid analysis, immunoassay, and molecular diagnosis.

Controlled Surface Enhanced Resonance Raman Scattering (SERRS) in Biological Environment

We report here the use of gold nanoparticle (AuNP) and gold nanostar (AuNS) assemblies modified with oligonucleotides for the detection of target DNA molecules through SERRS. SERS activities of assmblies consisted of 16 nm AuNPs, 30 nm AuNSs and 100 nm AuNSs were compared. Interaction of localized surface plasmon resonance (LSPR) of AuNP and AuNS assemblies were controlled through adjusting the distance between AuNPs/AuNSs which were realized by varying the length of oligonucleotide with various base sequence. Raman spectroscopies were measured with excitation wavelength of 633 nm. It was found that stronger Raman signal was recorded when AuNSs were used while weaker signals were obtained with AuNPs. This may attribute to AuNSs has tip-enhancement effect while AuNPs has no tips on surface, and AuNSs DNA probes can easily detect 10 nM target DNA. We also found that the Raman signal being stronger when the distance between nanoparticles is ∼3 nm than that of ∼6 nm and ∼12 nm. We envisage this study will achieve further insight into the mechanism of SERRS and provide a general approach for the ultrasensitive detection of biomolecules based on SERRS.

Magnetic Graphitic Nanocapsules for Programmed DNA Fishing and Detection

Graphene nanomaterials are typically used in biosensing applications, and they have been demonstrated as good fluorescence quenchers. While many conventional amplification platforms are available, developing new nanomaterials and establishing simple, enzyme-free and low-cost strategies for high sensitivity biosensing is still challenging. Therefore, in this work, a core-shell magnetic graphitic nanocapsule (MGN) material is synthesized and its capabilities for the detection of biomolecules are investigated. MGN combines the unique properties of graphene and magnetic particles into one simple and sensitive biosensing platform, which quenches around 98% of the dye fluorescence within minutes. Based on a programmed multipurpose DNA capturing and releasing strategy, the MGN sensing platform demonstrates an outstanding capacity to fish, enrich, and detect DNA. Target DNA molecules as low as 50 pM could be detected, which is 3-fold lower than the limit of detection commonly achieved by carbon nanotube and graphene-based fluorescent biosensors. Moreover, the MGN platform exhibits good sensing specificity against DNA mismatch tests. Overall, therefore, these magnetic graphitic nanocapsules demonstrate a promising tool for molecular disease diagnosis and biomedicine. This simple fishing and enrichment strategy may also be extended to other biological and environmental applications and systems.