Evaluation of silica resins for direct and efficient extraction of DNA from complex biological matrices in a miniaturized format

Characteristics of RNA Stabilizer RNApro for Peripheral Blood Collection

Peripheral blood is the most practical tissue for human immune system gene expression profiling because it is easily accessible, whereas the site of primary infection in certain diseases may not be easily accessible. Due to the ex vivo instability of RNA transcripts, a key challenge in the gene expression analysis of blood samples is the rapid sample handling and stabilization of the mRNA by adding an RNA preservative (PAXgeneTM Blood RNA Tubes, TempusTM Blood RNA tubes, RNAlater Stabilization Reagent, RNAgard® Blood Tubes). BioMole (Turin, Italy) has developed a novel blood stabilizer, called RNApro, in which RNA is stabilized during phlebotomy and sample storage. In this study, RNApro performance intended as RNA yield, integrity, and stability was evaluated. Our results show that blood samples stored at -80 °C and re-extracted after 7 years show no differences in terms of quantity, quality, and amplificability. The samples in the RNAlater stabilization solution can be stored at room temperature for up to one week or at 4 °C for up to one month. Similar results can also be observed for PAXgene tubes, Tempus tubes, and RNAgard tubes. In agreement with these data, the RNApro stabilization solution preserves the RNA from degradation for up to 1 month at 4 °C and 1 week at room temperature. RNApro can be stored indifferently at -80, -20, 4 °C, or room temperature for up to 2 months after, and then could be stored at -80 °C for up to seven years. In summary, our study is the first to analyze the performance of an RNA stabilizer called RNApro. We can conclude that several studies have shown significant differences in gene expression analysis when the sample was preserved in different RNA stabilizers. Therefore, it is desirable to standardize the method of nucleic acid conservation when comparing data from transcriptomic analyses.

Accelerated Electrophoretic Focusing and Purification of DNA Based on Synchronous Coefficient of Drag Alteration

Synchronous coefficient of drag alteration refers to a multidimensional transport mechanism where a net drift of molecules is achieved under a zero-time-average alternating motive force by perturbing their drag coefficient synchronously with the applied force. An electrophoretic form of the method is often applied to focus and purify nucleic acids in a gel under rotating electric fields. However, this method requires lengthy operation due to the use of limited field strengths. Here, using DNA as target molecules, we demonstrate that the operation time can be reduced from hours to minutes by replacing polymer gel with a microfabricated artificial sieve. We also describe an electrophoretic protocol that facilitates the collection of purified DNA from the sieve, which is shown to yield amplifiable DNA from crude samples including the lysates of cultured cells and whole blood. The sieve can be further equipped with nucleic acid amplification and detection functions for a point-of-care diagnostic application.

Application of microfluidic technologies in forensic analysis

The application of microfluidic technology in forensic medicine has steadily expanded over the last two decades due to the favorable features of low cost, rapidity, high throughput, user-friendliness, contamination-free, and minimum sample and reagent consumption. In this context, bibliometric methods were adopted to visualize the literature information contained in the Science Citation Index Expanded from 1989 to 2022, focusing on the co-occurrence analysis of forensic and microfluidic topics. A deep interpretation of the literature was conducted based on co-occurrence results, in which microfluidic technologies and their applications in forensic medicine, particularly forensic genetics, were elaborated. The purpose of this review is to provide an impartial evaluation of the utilization of microfluidic technology in forensic medicine. Additionally, the challenges and future trends of implementing microfluidic technology in forensic genetics are also addressed.

On the Application of Microfluidic-Based Technologies in Forensics: A Review

Microfluidic technology is a powerful tool to enable the rapid, accurate, and on-site analysis of forensically relevant evidence on a crime scene. This review paper provides a summary on the application of this technology in various forensic investigation fields spanning from forensic serology and human identification to discriminating and analyzing diverse classes of drugs and explosives. Each aspect is further explained by providing a short summary on general forensic workflow and investigations for body fluid identification as well as through the analysis of drugs and explosives. Microfluidic technology, including fabrication methodologies, materials, and working modules, are touched upon. Finally, the current shortcomings on the implementation of the microfluidic technology in the forensic field are discussed along with the future perspectives.

The emerging landscape of microfluidic applications in DNA data storage

DNA has been considered a promising alternative to the current solid-state devices for digital information storage. The past decade has witnessed tremendous progress in the field of DNA data storage contributed by researchers from various disciplines. However, the current development status of DNA storage is still far from practical use, mainly due to its high material cost and time consumption for data reading/writing, as well as the lack of a comprehensive, automated, and integrated system. Microfluidics, being capable of handling and processing micro-scale fluid samples in a massively paralleled and highly integrated manner, has gradually been recognized as a promising candidate for addressing the aforementioned issues. In this review, we provide a discussion on recent efforts of applying microfluidics to advance the development of DNA data storage. Moreover, to showcase the tremendous potential that microfluidics can contribute to this field, we will further highlight the recent advancements of applying microfluidics to the key functional modules within the DNA data storage workflow. Finally, we share our perspectives on future directions for how to continue the infusion of microfluidics with DNA data storage and how to advance toward a truly integrated system and reach real-life applications.

Rapid and inexpensive method of PCR ready DNA isolation from human peripheral blood and saliva

BACKGROUND

The isolation of nucleic acids is a frequently performed procedure in the molecular biology area. Although several rapid DNA isolation techniques from human peripheral blood and saliva have been developed, there are still some disadvantages - volume, time, cost, and yield are a few notable ones.

OBJECTIVE

We aim to develop a rapid and inexpensive method to isolate high-molecular-weight genomic DNA from human peripheral blood and saliva that can be used for molecular biology experiments.

METHODS

Five DNA isolation methods with slightly varying protocols were used. High-quality DNA obtained from one specific method was further amplified by PCR and the template with good amplification was further used for performing RFLP and sequencing.

RESULTS

Out of 5 different isolation methods (R1 to R5), DNA obtained from the R4 was of good quality (molecular weight is > 10 kb and 260/280 ratio is 1.89 ± 0.2), which allows successful PCR amplification and good separation in Restriction Fragment Length Polymorphism analysis. Sequencing by the Sanger Sequencing produced a good readable sequence of an amplified fragment from Method R4 DNA.

CONCLUSION

In the present study we have developed a simple, rapid, and cost-effective DNA isolation method, which uses low sample volume and yields good quantity and high-quality product. The DNA obtained is highly fit for molecular genetics research applications.

A microfluidic platform for high-purity cell free DNA extraction from plasma for non-invasive prenatal testing

OBJECTIVES

Increase the yield and purity of cell-free DNA (cfDNA) extracted from plasma for non-invasive prenatal testing (NIPT) as inefficiencies in this extraction and purification can dramatically affect the sensitivity and specificity of the test.

METHODS

This work integrates cfDNA extraction from plasma with a microfluidic chip platform by combining magnetic bead-based extraction and electroosmotic flow on the microfluidic chip. Various wash buffers and voltage conditions were simulated using COMSOL Multiphysics Modeling and tested experimentally.

RESULTS

When performing the first wash step of this assay on the microfluidic chip with 300 V applied across the channel there was a six-fold increase in the A₂₆₀ /A₂₃₀ ratio showing a significant improvement (p value 0.0005) in the purity of the extracted sample all while maintaining a yield of 68.19%. These values are critical as a high yield results in more sample to analyze and an increase in A₂₆₀ /A₂₃₀ ratio corresponds to a decrease in salt contaminants such as guanidinium thiocyanate which can interfere with downstream processes during DNA library preparation and potentially hinder the NIPT screening results.

CONCLUSIONS

This technique has the potential to improve NIPT outcomes and other clinically relevant workflows that use cfDNA as an analyte such as cancer detection.

Multifunctional magnetic nanoparticle cloud assemblies for in situ capture of bacteria and isolation of microbial DNA

We investigate the formation of suspended magnetic nanoparticle (MNP) assemblies (M-clouds) and their use for in situ bacterial capture and DNA extraction. M-clouds are obtained as a result of magnetic field density variations when magnetizing an array of micropillars coated with a soft ferromagnetic NiP layer. Numerical simulations suggest that the gradient in the magnetic field created by the pillars is four orders of magnitude higher than the gradient generated by the external magnets. The pillars therefore serve as the sole magnetic capture sites for MNPs which accumulate on opposite sides of each pillar facing the magnets. Composed of loosely aggregated MNPs, the M-cloud can serve as a porous capture matrix for target analyte flowing through the array. The concept is demonstrated by using a multifunctional M-cloud comprising immunomagnetic NPs (iMNPs) for capture of Escherichia coli O157:H7 from river water along with silica-coated NPs for subsequent isolation and purification of microbial DNA released upon bacterial lysis. Confocal microscopy imaging of fluorescently labeled iMNPs and E. coli O157:H7 reveals that bacteria are trapped in the M-cloud region between micropillars. Quantitative assessment of in situ bacterial capture, lysis and DNA isolation using real-time polymerase chain reaction shows linear correlation between DNA output and input bacteria concentration, making it possible to confirm E. coli 0157:H7 at 10³ cells per mL. The M-cloud method further provides one order of magnitude higher DNA output concentrations than incubation of the sample with iMNPs in a tube for an equivalent period of time (e.g., 10 min). Results from assays performed in the presence of Listeria monocytogenes (at 10⁶ cells per mL each) suggest that non-target organisms do not affect on-chip E. coli capture, DNA extraction efficiency and quality of the eluted sample.

Advances in sulfur mustard-induced DNA adducts: Characterization and detection

Sulfur mustard (SM) is a blister chemical warfare agent with severe cytotoxicity and genotoxicity. It can extensively alkylate important macromolecules in organisms, such as proteins, DNA, and lipids, and produce a series of metabolites, among which the characteristic ones can be used as biomarkers. The exact toxicological mechanisms of SM remain unclear but mainly involve the DNA lesions induced by alkylation and oxidative stress caused by glutathione depletion. Various methods have been used to analyze DNA damage caused by SM. Among these methods, liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology stands out and makes it possible to observe damage in view of biomarkers induced by SM. Sample preparation is critical for detection by LC-MS/MS and mainly includes DNA isolation, adduct hydrolysis, and adduct purification. Moreover, optimization of chromatographic conditions, selection of MS transitions, and quantitative strategies are also essential. SM-DNA adducts are generally considered to be N⁷-HETEG, O⁶-HETEG, N⁷-BisG, and N³-HETEA. This article proposes some other possibilities of SM-DNA adducts for the identification of SM genotoxicity.

On-site genetic analysis for species identification using lab-on-a-chip

This paper presents a microfluidic device capable of performing genetic analysis on dung samples to identify White Rhinoceros (Ceratotherium simum). The development of a microfluidic device, which can be used in the field, offers a portable and cost-effective solution for DNA analysis and species identification to aid conservation efforts. Optimization of the DNA extraction processes produced equivalent yields compared to conventional kit-based methods within just 5 minutes. The use of a color-changing loop-mediated isothermal amplification reaction for simultaneous detection of the cytochrome B sequence of C. simum enabled positive results to be obtained within as little as 30 minutes. Field testing was performed at Knowsley Safari to demonstrate real-world applicability of the microfluidic device for testing of biological samples.

Separation of Biological Entities From Human Blood by Using Magnetic Nanocomposites Obtained From Zeolite Precursors

In this work, three novel magnetic metal–ceramic nanocomposites were obtained by thermally treating Fe-exchanged zeolites (either A or X) under reducing atmosphere at relatively mild temperatures (750–800 °C). The so-obtained materials were thoroughly characterized from the point of view of their physico-chemical properties and, then, used as magnetic adsorbents in the separation of the target gene factors V and RNASE and of the Staphylococcus aureus bacteria DNA from human blood. Such results were compared with those obtained by using a top ranking commercial separation system (namely, SiMAG-N-DNA by Chemicell). The results obtained by using the novel magnetic adsorbents were similar to (or even better than) those obtained by using the commercial system, both during manual and automated separations, provided that a proper protocol was adopted. Particularly, the novel magnetic adsorbents showed high sensitivity during tests performed with small volumes of blood. Finally, the feasible production of such magnetic adsorbents by an industrial process was envisaged as well.

Adsorption and desorption of DNA-functionalized beads in glass microfluidic channels

Integrated microfluidic devices for the purification, amplification, and detection of nucleic acids are a prevalent area of research due to their potential for miniaturization, assay integration, and increased efficiency over benchtop assays. These devices frequently contain micrometer-sized magnetic beads with a large surface area for the capture and manipulation of biological molecules such as DNA and RNA. Although magnetic beads are a standard tool for many biological assays, beads functionalized with biological molecules can adhere to microchannel walls and prevent further manipulation of the beads within the channel. Here, we analyze the effects of solution composition, microchannel hydrophobicity, and bead surface hydrophobicity on DNA-functionalized bead adhesion in a borosilicate glass microfluidic device. Bead adhesion is primarily a result of adsorption of the bead-linked DNA molecule to the microchannel wall; >81% of beads are consistently removed when not functionalized with DNA. Hydrophobicities of both the microchannel walls and the microbead surface are the primary determinants of bead adhesion, rather than electrostatic interactions and ion bridging. Surprisingly, DNA-functionalized bead adhesion in a standard RNA amplification solution was virtually eliminated by using hydrophobic microbeads with hydrophobic microchannel walls; under such conditions, 96.6 ± 1.6% of the beads were removed in one 43 nl/s, 10-min wash. The efficiency of a downstream RNA amplification reaction using DNA-functionalized beads did not appear to be affected by the hydrophobicity of the microbead surface. These findings can be applied to assays that require the efficient use of magnetic beads in DNA-based microfluidic assays.

Centrifugation-Assisted Immiscible Fluid Filtration for Dual-Bioanalyte Extraction

The extraction of bioanalytes is the first step in many diagnostic and analytical assays. However, most bioanalyte extraction methods require extensive dilution-based washing processes that are not only time-consuming and laborious but can also result in significant sample loss, limiting their applications in rare sample analyses. Here, we present a method that enables the efficient extraction of multiple different bioanalytes from rare samples (down to 10 cells) without washing-centrifugation-assisted immiscible fluid filtration (CIFF). CIFF utilizes centrifugal force to drive the movement of analyte-bound glass microbeads from an aqueous sample into an immiscible hydrophobic solution to perform an efficient, simple, and nondilutive extraction. The method can be performed using conventional polymerase chain reaction (PCR) tubes with no requirement of specialized devices, columns, or instruments, making it broadly accessible and cost-effective. The CIFF process can effectively remove approximately 99.5% of the aqueous sample in one extraction with only 0.5% residual carryover, whereas a traditional "spin-down and aspirate" operation results in a higher 3.6% carryover. Another unique aspect of CIFF is its ability to perform two different solid-phase bioanalytes extractions simultaneously within a single vessel without fractionating the sample or performing serial extractions. Here we demonstrate efficient mRNA and DNA extraction from low-input samples (down to 10 cells) with slightly higher to comparable recovery compared to a traditional column-based extraction technique and the simultaneous extraction of two different proteins in the same tube using CIFF.

A new approach to preparation of antisense oligonucleotide samples with microextraction by packed sorbent

Our research focused on applying microextraction by packed sorbent to extracting antisense oligonucleotides from serum samples. The tested sorbents included poly(styrene-co-divinylbenzene), octyl, octadecyl, and unmodified silica gel. As nonpolar sorbents were used for highly-polar molecules, this required ion-pair mode. Comprehensive optimization of extraction conditions was performed for 20-mer phosphorothioate oligonucleotide. Several parametres - the number of "draw-eject" cycles during the conditioning and load step, the amine type and concentration, and the volume of elution mixture - and the influence they had on recovery were studied for nonpolar sorbents, which made it possible to obtain high (ca. 90%) recovery values. The most influential parameter turned out to be the volume of elution mixture. Similar optimization was performed for silica sorbents; however, despite optimization of various parameters, the recovery values stayed relatively low. The optimized procedures for nonpolar sorbents were applied in extraction of six different oligonucleotides of various length and with different structure modifications. The highest recoveries were obtained for octyl and octadecyl sorbents, ranging between 80-99%. The developed microextraction method was used to extract phosphorothioate and 2'-O-(2-methoxyethyl) oligonucleotides and their two synthetic metabolites from enriched human plasma, with recoveries around 70-80%.

Silicon µPCR Chip for Forensic STR Profiling with Hybeacon Probe Melting Curves

The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit tremendously from having DNA based information available in the first hours rather than days or weeks. However, due to the complexity and time-consuming nature of standard DNA fingerprinting methods, rapid and automated analyses are hard to achieve. We here demonstrate the implementation of an alternative DNA fingerprinting method in a single microchip. By combining PCR amplification and HyBeacon melting assays in a silicon Lab-on-a-chip (LoC), a significant step towards rapid on-site DNA fingerprinting is taken. The small form factor of a LoC reduces reagent consumption and increases portability. Additional miniaturization is achieved through an integrated heating element covering 24 parallel micro-reactors with a reaction volume of 0.14 µl each. The high level of parallelization allows the simultaneous analysis of 4 short tandem repeat (STR) loci and the amelogenin gender marker commonly included in forensic DNA analysis. A reference and crime scene sample can be analyzed simultaneously for direct comparison. Importantly, by using industry-standard semiconductor manufacturing processes, mass manufacturability can be guaranteed. Following assay design and optimization, complete 5-loci profiles could be robustly generated on-chip that are on par with those obtained using conventional benchtop real-time PCR thermal cyclers. Together, our results are an important step towards the development of commercial, mass-produced, portable devices for on-site testing in forensic DNA analysis.

Microfluidic approaches for cell-based molecular diagnosis

The search for next-generation biomarkers has enabled cell-based diagnostics in a number of disciplines ranging from oncology to pharmacogenetics. However, cell-based diagnostics are still far from clinical reality due to the complex assays and associated protocols which typically require cell isolation, lysis, DNA extraction, amplification, and detection steps. Leveraging recent advances in microfluidics, many biochemical assays have been translated onto microfluidic platforms. We have compared and summarized recent advances in modular approaches toward the realization of fully-integrated, cell-based molecular diagnostics for clinical and point-of-care applications.

Rapid Regeneration and Reuse of Silica Columns from PCR Purification and Gel Extraction Kits

Silica columns from PCR purification and gel extraction kits are widely used in laboratories worldwide to assist in gene cloning. However, the use of these columns can generate plastic waste that has an environmental impact due to their one-off design and massive consumption. Thus, it is important to develop a novel method that can reduce the utilization of silica columns but not affect research efficiency. In this study, various chemical and nonchemical reagents were used to eliminate residual DNA within used columns from PCR purification and gel extraction kits. We show that phosphoric acid is the most effective reagent among those tested to remove DNA contamination from used columns. Columns regenerated using 1 M phosphoric acid have a DNA purification capability that is comparable to that of fresh columns. We demonstrate that silica columns can be regenerated and reused a minimum of five times. The lab-made buffers are compatible with the regenerated columns for DNA purification, and DNA that is prepared with the regenerated columns can be used for gene cloning without affecting the gene cloning efficiency. Thus, the use of this novel method greatly reduces the production of laboratory waste and benefits numerous laboratories worldwide.

NiO Nanoparticles for Exceptionally Stable DNA Adsorption and Its Extraction from Biological Fluids

Selective extraction of a small amount of nucleic acids from complex biological samples containing a high concentration of proteins is critical for bioanalytical chemistry. A number of previously published studies have focused on long, double-stranded DNA such as plasmid DNA. On the other hand, we are interested in short oligonucleotides. Nucleic acids have a negatively charged phosphate backbone that interacts with metal oxides strongly, and this may be used to distinguish them from proteins. In this work, a few metal oxide nanoparticles were screened, including NiO, CoO, ZnO, TiO₂, CeO₂, and Fe₃O₄ for DNA recovery. NiO had the highest DNA adsorption efficiency from mixtures containing bovine serum albumin or human blood serum. The adsorption of DNA by NiO was further characterized as a function of the pH, salt concentration, DNA length, and DNA sequence. The adsorption mechanism was studied by adding competing chemicals or denaturing agents. A striking observation was the extremely high adsorption affinity of NiO, much higher than that of the other tested oxides. Polyphosphate was the most effective agent for displacing adsorbed DNA, whereas simple inorganic phosphate was less effective. NiO was able to concentrate DNA from a serum mixture by 33- to 55-fold, depending on the serum concentration. NiO is thus a promising candidate for extracting DNA from biological samples.

A review on microscale polymerase chain reaction based methods in molecular diagnosis, and future prospects for the fabrication of fully integrated portable biomedical devices

Since the advent of microfabrication technology and soft lithography, the lab-on-a-chip concept has emerged as a state-of-the-art miniaturized tool for conducting the multiple functions associated with micro total analyses of nucleic acids, in series, in a seamless manner with a miniscule volume of sample. The enhanced surface-to-volume ratio inside a microchannel enables fast reactions owing to increased heat dissipation, allowing rapid amplification. For this reason, PCR has been one of the first applications to be miniaturized in a portable format. However, the nature of the basic working principle for microscale PCR, such as the complicated temperature controls and use of a thermal cycler, has hindered its total integration with other components into a micro total analyses systems (μTAS). This review (with 179 references) surveys the diverse forms of PCR microdevices constructed on the basis of different working principles and evaluates their performances. The first two main sections cover the state-of-the-art in chamber-type PCR microdevices and in continuous-flow PCR microdevices. Methods are then discussed that lead to microdevices with upstream sample purification and downstream detection schemes, with a particular focus on rapid on-site detection of foodborne pathogens. Next, the potential for miniaturizing and automating heaters and pumps is examined. The review concludes with sections on aspects of complete functional integration in conjunction with nanomaterial based sensing, a discussion on future prospects, and with conclusions. Graphical abstract In recent years, thermocycler-based PCR systems have been miniaturized to palm-sized, disposable polymer platforms. In addition, operational accessories such as heaters and mechanical pumps have been simplified to realize semi-automatted stand-alone portable biomedical diagnostic microdevices that are directly applicable in the field. This review summarizes the progress made and the current state of this field.

DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods

This review covers a developmental progression on early to modern taxonomy at cellular level following the advent of electron microscopy and the advancement in deoxyribonucleic acid (DNA) extraction for expatiation of biological classification at DNA level. Here, we discuss the fundamental values of conventional chemical methods of DNA extraction using liquid/liquid extraction (LLE) followed by development of solid-phase extraction (SPE) methods, as well as recent advances in microfluidics device-based system for DNA extraction on-chip. We also discuss the importance of DNA extraction as well as the advantages over conventional chemical methods, and how Lab-on-a-Chip (LOC) system plays a crucial role for the future achievements.

Rapid Nucleic Acid Extraction and Purification Using a Miniature Ultrasonic Technique

Miniature ultrasonic lysis for biological sample preparation is a promising technique for efficient and rapid extraction of nucleic acids and proteins from a wide variety of biological sources. Acoustic methods achieve rapid, unbiased, and efficacious disruption of cellular membranes while avoiding the use of harsh chemicals and enzymes, which interfere with detection assays. In this work, a miniature acoustic nucleic acid extraction system is presented. Using a miniature bulk acoustic wave (BAW) transducer array based on 36° Y-cut lithium niobate, acoustic waves were coupled into disposable laminate-based microfluidic cartridges. To verify the lysing effectiveness, the amount of liberated ATP and the cell viability were measured and compared to untreated samples. The relationship between input power, energy dose, flow-rate, and lysing efficiency were determined. DNA was purified on-chip using three approaches implemented in the cartridges: a silica-based sol-gel silica-bead filled microchannel, nucleic acid binding magnetic beads, and Nafion-coated electrodes. Using E. coli, the lysing dose defined as ATP released per joule was 2.2× greater, releasing 6.1× more ATP for the miniature BAW array compared to a bench-top acoustic lysis system. An electric field-based nucleic acid purification approach using Nafion films yielded an extraction efficiency of 69.2% in 10 min for 50 µL samples.

Sample-to-answer on molecular diagnosis of bacterial infection using integrated lab--on--a--disc

Sepsis by bacterial infection causes high mortality in patients in intensive care unit (ICU). Rapid identification of bacterial infection is essential to ensure early appropriate administration of antibiotics to save lives of patients, yet the present benchtop molecular diagnosis is time-consuming and labor-intensive, which limits the treatment efficiency especially when the number of samples to be tested is extensive. Therefore, we hereby report a microfluidic platform lab-on-a-disc (LOAD) to provide a sample-to-answer solution. Our LOAD customized design of microfluidic channels allows automation to mimic sequential analytical steps in benchtop environment. It relies on a simple but controllable centrifugation force for the actuation of samples and reagents. Our LOAD system performs three major functions, namely DNA extraction, isothermal DNA amplification and real-time signal detection, in a predefined sequence. The disc is self-contained for conducting sample heating with chemical lysis buffer and silica microbeads are employed for DNA extraction from clinical specimens. Molecular diagnosis of specific target bacteria DNA sequences is then performed using a real-time loop-mediated isothermal amplification (RT-LAMP) with SYTO-9 as the signal reporter. Our LOAD system capable of bacterial identification of Mycobacterium tuberculosis (TB) and Acinetobacter baumanii (Ab) with the detection limits 103cfu/mL TB in sputum and 102cfu/mL Ab in blood within 2h after sample loading. The reported LOAD based on an integrated approach should address the growing needs for rapid point-of-care medical diagnosis in ICU.

Low concentration DNA extraction and recovery using a silica solid phase

DNA extraction from clinical samples is commonly achieved with a silica solid phase extraction column in the presence of a chaotrope. Versions of these protocols have been adapted for point of care (POC) diagnostic devices in miniaturized platforms, but commercial kits require a high amount of input DNA. Thus, when the input clinical sample contains less than 1 μg of total DNA, the target-specific DNA recovery from most of these protocols is low without supplementing the sample with exogenous carrier DNA. In fact, many clinical samples used in the development of POC diagnostics often exhibit target DNA concentrations as low as 3 ng/mL. With the broader goal of improving the yield and efficiency of nucleic acid-based POC devices for dilute samples, we investigated both DNA adsorption and recovery from silica particles by using 1 pg- 1 μg of DNA with a set of adsorption and elution buffers ranging in pH and chaotropic presence. In terms of adsorption, we found that low pH and the presence of chaotropic guanidinium thiocyanate (GuSCN) enhanced DNA-silica adsorption. When eluting with a standard low-salt, high-pH buffer, > 70% of DNA was unrecoverable, except when DNA was initially adsorbed with 5 M GuSCN at pH 5.2. Unrecovered DNA was either not initially adsorbed or irreversibly bound on the silica surface. Recovery was improved when eluting with 95°C formamide and 1 M NaOH, which suggested that DNA-silica-chaotrope interactions are dominated by hydrophobic interactions and hydrogen bonding. While heated formamide and NaOH are non-ideal elution buffers for practical POC devices, the salient results are important for engineering a set of optimized reagents that could maximize nucleic acid recovery from a microfluidic DNA-silica-chaotrope system.

Integrated DNA and RNA extraction using magnetic beads from viral pathogens causing acute respiratory infections

Current extraction methods often extract DNA and RNA separately, and few methods are capable of co-extracting DNA and RNA from sputum. We established a nucleic acid co-extraction method from sputum based on magnetic beads and optimized the method by evaluating influencing factors, such as the guanidinium thiocyanate (GTC) and dithiothreitol (DTT) concentrations, magnetic bead amount, incubation temperature, lysis buffer pH and RNA carrier type. The feasibility of the simultaneous nucleic acid co-extraction method was evaluated by amplifying DNA and RNA viruses from a single clinical specimen with a multiplex RT-qPCR method. Both DNA and RNA were most efficiently extracted when the GTC and DTT concentrations were 2.0 M and 80 mM, respectively, 20 μl magnetic beads were added, the incubation temperature was 80 °C, the pH was 8 or 9, and RNA carrier A was used. Therefore, we established a simple method to extract nucleic acids from two important respiratory viruses compared with other commercial kits. This magnetic beads-based co-extraction method for sputum followed by a multiplex RT-qPCR can rapidly and precisely detect DNA and RNA viruses from a single clinical specimen and has many advantages, such as decreased time, low cost, and a lack of harmful chemicals.

Chitosan-Modified Filter Paper for Nucleic Acid Extraction and "in Situ PCR" on a Thermoplastic Microchip

Plastic microfluidic devices with embedded chitosan-modified Fusion 5 filter paper (unmodified one purchased from GE Healthcare) have been successfully developed for DNA extraction and concentration, utilizing two different mechanisms for DNA capture: the physical entanglement of long-chain DNA molecules with the fiber matrix of the filter paper and the electrostatic adsorption of DNA to the chitosan-modified filter fibers. This new method not only provided a high DNA extraction efficiency at a pH of 5 by synergistically combining these two capture mechanisms together, but also resisted the elution of DNA from filters at a pH > 8 due to the entanglement of DNA with fibers. As a result, PCR buffers can be directly loaded into the extraction chamber for "in situ PCR", in which the captured DNA were used for downstream analysis without any loss. We demonstrated that the capture efficiencies of a 3-mm-diameter filter disc in a microchip were 98% and 95% for K562 human genomic DNA and bacteriophage λ-DNA, respectively. The washes with DI water, PCR mixture, and TE buffer cannot elute the captured DNA. In addition, the filter disc can enrich 62% of λ-DNA from a diluted sample (0.05 ng/μL), providing a concentration factor more than 30-fold. Finally, a microdevice with a simple two-chamber structure was developed for on-chip cell lysis, DNA extraction, and 15-plex short tandem repeat amplification from blood. This DNA extraction coupled with "in situ PCR" has great potential to be utilized in fully integrated microsystems for rapid, near-patient nucleic acid testing.

A novel miniaturized biofilter based on silicon micropillars for nucleic acid extraction

New miniaturised microfluidic biofilter (BF) devices based on silicon micropillars have been developed and tested regarding their ability to extract HBV (Hepatitis B Virus) bacterial DNA from biological sample solutions.

A Simple Thermoplastic Substrate Containing Hierarchical Silica Lamellae for High-Molecular-Weight DNA Extraction

An inexpensive, magnetic thermoplastic nanomaterial is developed utilizing a hierarchical layering of micro- and nanoscale silica lamellae to create a high-surface-area and low-shear substrate capable of capturing vast amounts of ultrahigh-molecular-weight DNA. Extraction is performed via a simple 45 min process and is capable of achieving binding capacities up to 1 000 000 times greater than silica microparticles.

Microfluidic Devices for Forensic DNA Analysis: A Review

Microfluidic devices may offer various advantages for forensic DNA analysis, such as reduced risk of contamination, shorter analysis time and direct application at the crime scene. Microfluidic chip technology has already proven to be functional and effective within medical applications, such as for point-of-care use. In the forensic field, one may expect microfluidic technology to become particularly relevant for the analysis of biological traces containing human DNA. This would require a number of consecutive steps, including sample work up, DNA amplification and detection, as well as secure storage of the sample. This article provides an extensive overview of microfluidic devices for cell lysis, DNA extraction and purification, DNA amplification and detection and analysis techniques for DNA. Topics to be discussed are polymerase chain reaction (PCR) on-chip, digital PCR (dPCR), isothermal amplification on-chip, chip materials, integrated devices and commercially available techniques. A critical overview of the opportunities and challenges of the use of chips is discussed, and developments made in forensic DNA analysis over the past 10–20 years with microfluidic systems are described. Areas in which further research is needed are indicated in a future outlook.

Sequence-Specific Electrical Purification of Nucleic Acids with Nanoporous Gold Electrodes

Nucleic-acid-based biosensors have enabled rapid and sensitive detection of pathogenic targets; however, these devices often require purified nucleic acids for analysis since the constituents of complex biological fluids adversely affect sensor performance. This purification step is typically performed outside the device, thereby increasing sample-to-answer time and introducing contaminants. We report a novel approach using a multifunctional matrix, nanoporous gold (np-Au), which enables both detection of specific target sequences in a complex biological sample and their subsequent purification. The np-Au electrodes modified with 26-mer DNA probes (via thiol-gold chemistry) enabled sensitive detection and capture of complementary DNA targets in the presence of complex media (fetal bovine serum) and other interfering DNA fragments in the range of 50-1500 base pairs. Upon capture, the noncomplementary DNA fragments and serum constituents of varying sizes were washed away. Finally, the surface-bound DNA-DNA hybrids were released by electrochemically cleaving the thiol-gold linkage, and the hybrids were iontophoretically eluted from the nanoporous matrix. The optical and electrophoretic characterization of the analytes before and after the detection-purification process revealed that low target DNA concentrations (80 pg/μL) can be successfully detected in complex biological fluids and subsequently released to yield pure hybrids free of polydisperse digested DNA fragments and serum biomolecules. Taken together, this multifunctional platform is expected to enable seamless integration of detection and purification of nucleic acid biomarkers of pathogens and diseases in miniaturized diagnostic devices.

One-step purification and concentration of DNA in porous membranes for point-of-care applications

The emergence of rapid, user-friendly, point-of-care (POC) diagnostic systems is paving the way for better disease diagnosis and control. Lately, there has been a strong emphasis on developing molecular-based diagnostics due to their potential for greatly increased sensitivity and specificity. One of the most critical steps in developing practical diagnostic systems is the ability to perform sample preparation, especially the purification of nucleic acids (NA), at the POC. As such, we have developed a simple-to-use, inexpensive, and disposable sample preparation system for in-membrane purification and concentration of NAs. This system couples lateral flow in a porous membrane with chitosan, a linear polysaccharide that captures NAs via anion exchange chromatography. The system can also substantially concentrate the NAs. The combination of these capabilities can be used on a wide range of sample types, which are prepared for use in downstream processes, such as qPCR, without further purification.

Optical Imaging of Paramagnetic Bead-DNA Aggregation Inhibition Allows for Low Copy Number Detection of Infectious Pathogens

DNA-paramagnetic silica bead aggregation in a rotating magnetic field facilitates the quantification of DNA with femtogram sensitivity, but yields no sequence-specific information. Here we provide an original description of aggregation inhibition for the detection of DNA and RNA in a sequence-specific manner following loop-mediated isothermal amplification (LAMP). The fragments generated via LAMP fail to induce chaotrope-mediated bead aggregation; however, due to their ability to passivate the bead surface, they effectively inhibit bead aggregation by longer 'trigger' DNA. We demonstrate the utility of aggregation inhibition as a method for the detection of bacterial and viral pathogens with sensitivity that approaches single copies of the target. We successfully use this methodology for the detection of notable food-borne pathogens Escherichia coli O157:H7 and Salmonella enterica, as well as Rift Valley fever virus, a weaponizable virus of national security concern. We also show the concentration dependence of aggregation inhibition, suggesting the potential for quantification of target nucleic acid in clinical and environmental samples. Lastly, we demonstrate the ability to rapidly detect infectious pathogens by utilizing a cell phone and custom-written application (App), making this novel detection modality fully portable for point-of-care use.

Active pneumatic control of centrifugal microfluidic flows for lab-on-a-chip applications

This paper reports a novel method of controlling liquid motion on a centrifugal microfluidic platform based on the integration of a regulated pressure pump and a programmable electromechanical valving system. We demonstrate accurate control over the displacement of liquids within the system by pressurizing simultaneously multiple ports of the microfluidic device while the platform is rotating at high speed. Compared to classical centrifugal microfluidic platforms where liquids are solely driven by centrifugal and capillary forces, the method presented herein adds a new degree of freedom for fluidic manipulation, which represents a paradigm change in centrifugal microfluidics. We first demonstrate how various core microfluidic functions such as valving, switching, and reverse pumping (i.e., against the centrifugal field) can be easily achieved by programming the pressures applied at dedicated access ports of the microfluidic device. We then show, for the first time, that the combination of centrifugal force and active pneumatic pumping offers the possibility of mixing fluids rapidly (~0.1 s) and efficiently based on the creation of air bubbles at the bottom of a microfluidic reservoir. Finally, the suitability of the developed platform for performing complex bioanalytical assays in an automated fashion is demonstrated in a DNA harvesting experiment where recovery rates of about 70% were systematically achieved. The proposed concept offers the interesting prospect to decouple basic microfluidic functions from specific material properties, channel dimensions and fabrication tolerances, surface treatments, or on-chip active components, thus promoting integration of complex assays on simple and low-cost microfluidic cartridges.

Extraction of DNA by magnetic ionic liquids: tunable solvents for rapid and selective DNA analysis

DNA extraction represents a significant bottleneck in nucleic acid analysis. In this study, hydrophobic magnetic ionic liquids (MILs) were synthesized and employed as solvents for the rapid and efficient extraction of DNA from aqueous solution. The DNA-enriched microdroplets were manipulated by application of a magnetic field. The three MILs examined in this study exhibited unique DNA extraction capabilities when applied toward a variety of DNA samples and matrices. High extraction efficiencies were obtained for smaller single-stranded and double-stranded DNA using the benzyltrioctylammonium bromotrichloroferrate(III) ([(C8)3BnN(+)][FeCl3Br(-)]) MIL, while the dicationic 1,12-di(3-hexadecylbenzimidazolium)dodecane bis[(trifluoromethyl)sulfonyl]imide bromotrichloroferrate(III) ([(C16BnIM)2C12(2+)][NTf2(-), FeCl3Br(-)]) MIL produced higher extraction efficiencies for larger DNA molecules. The MIL-based method was also employed for the extraction of DNA from a complex matrix containing albumin, revealing a competitive extraction behavior for the trihexyl(tetradecyl)phosphonium tetrachloroferrate(III) ([P6,6,6,14(+)][FeCl4(-)]) MIL in contrast to the [(C8)3BnN(+)][FeCl3Br(-)] MIL, which resulted in significantly less coextraction of albumin. The MIL-DNA method was employed for the extraction of plasmid DNA from bacterial cell lysate. DNA of sufficient quality and quantity for polymerase chain reaction (PCR) amplification was recovered from the MIL extraction phase, demonstrating the feasibility of MIL-based DNA sample preparation prior to downstream analysis.