Thread-powered cell lysis and isotachophoresis: unlocking microbial DNA for diverse molecular applications

Central to the domain of molecular biology resides the foundational process of DNA extraction and purification, a cornerstone underpinning a myriad of pivotal applications. In this research, we introduce a DNA extraction and purification technique leveraging polypropylene (PP) threads. The process commences with robust cell lysis achieved through the vigorous agitation of interwoven PP threads. The friction between the threads facilitates cell lysis especially those microbes having tough cell wall. For purification of DNA, thread-based isotachophoresis was employed which makes the whole process swift and cost-effective. Lysed cell-laden threads were submerged in a trailing electrolyte which separated DNA from other cellular contents. The process was performed with a tailored ITP device. An electric field directs DNA, cell debris, trailing electrolyte, and leading electrolyte toward the anode. Distinct ion migration resulted in DNA concentrating on the PP thread's anode-proximal region. The SYBR green dye is used to visualize DNA as a prominent green zone under blue light. The purified DNA exhibits high purity levels of 1.82 ± 0.1 (A260/A280), making it suitable for various applications aiming at nucleic acid detection.

Bottom-Up Analysis of Proteins by Peptide Mass Fingerprinting with tCITP-CZE-ESI-TOF MS After Tryptic Digest

The identification of proteins in samples of moderate to complex composition is primarily done by bottom-up approaches. Therefore, proteins are enzymatically digested, mostly by trypsin, and the resulting peptides are then separated prior to their transfer to a mass spectrometer. The following protocol portrays a bottom-up method, which was optimized for the application of CZE-ESI-TOF MS. Protein denaturation is achieved by addition of 2,2,2-trifluoroethanol (TFE) and heat treatment. Afterwards, disulfide bonds are reduced with tris-(2-carboxyethyl)phosphine (TCEP) and subsequently alkylated with iodoacetamide (IAA). The tryptic digest is performed in an ammonium bicarbonate buffer at pH 8.0. The digested protein sample is then concentrated in-capillary by transient capillary isotachophoresis (tCITP) with subsequent CZE separation of tryptic peptides in an acidic background electrolyte. Hyphenation to a time-of-flight (TOF) mass spectrometer is carried out by a triple-tube coaxial sheath flow interface, which uses electrospray ionization (ESI). Peptide identification is done by peptide mass fingerprinting (PMF). The protocol is outlined exemplarily for a model protein, i.e., bovine β-lactoglobulin A.

Simultaneous Determination of Ciprofloxacin and Ofloxacin in Animal Tissues with the Use of Capillary Electrophoresis with Transient Pseudo-Isotachophoresis

We have developed a precise and accurate method for the determination of ciprofloxacin and ofloxacin in meat tissues. Our method utilizes capillary electrophoresis with a transient pseudo-isotachophoresis mechanism and liquid–liquid extraction during sample preparation. For our experiment, a meat tissue sample was homogenized in pH 7.00 phosphate buffer at a ratio of 1:10 (tissue mass: buffer volume; g/mL). The extraction of each sample was carried out twice for 15 min with 600 µL of a mixture of dichloromethane and acetonitrile at a 2:1 volume ratio. We then conducted the electrophoretic separation at a voltage of 16 kV and a temperature of 25 °C using a background electrolyte of 0.1 mol/L phosphate–borate (pH 8.40). We used the UV detection at 288 nm. The experimentally determined LOQs for ciprofloxacin and ofloxacin were 0.27 ppm (0.8 nmol/g tissue) and 0.11 ppm (0.3 nmol/g tissue), respectively. The calibration curves exhibited linearity over the tested concentration range of 2 to 10 nmol/g tissue for both analytes. The relative standard deviation of the determination did not exceed 15%, and the recovery was in the range of 85–115%. We used the method to analyze various meat tissues for their ciprofloxacin and ofloxacin contents.

Thread-based isotachophoresis for DNA extraction and purification from biological samples

A rapid, low-cost, and disposable microfluidic thread-based isotachophoresis method was developed for the purification and preconcentration of nucleic acids from biological samples, prior to their extraction and successful analysis using quantitative polymerase chain reaction (qPCR). This approach extracts and concentrates protein-free DNA from the terminating electrolyte buffer, via a continuous sampling approach, resulting in significant focussing of the extracted DNA upon a 6 cm length nylon thread. The platform was optimised using the preconcentration of a fluorescent dye, showing a 600-fold concentration capacity within <5 min. The system was then applied to the one-step extraction of lambda DNA - an E. coli bacteriophage - spiked into whole blood, exhibiting the exclusion of PCR inhibitors. The extraction efficiency from the thread material following concentration was consistent, between 94.4-113.9%. The determination of lambda DNA in whole blood was achieved within a linear range of 1.0-1 × 105 fg μL-1 (20-2 × 106 copies per μL). This technique demonstrates great potential for the development of thread-based affordable analytical and diagnostic devices based upon DNA and RNA isolation.

HIV detection from human serum with paper-based isotachophoretic RNA extraction and reverse transcription recombinase polymerase amplification

The number of people living with HIV continues to increase with the current total near 38 million, of which about 26 million are receiving antiretroviral therapy (ART). These treatment regimens are highly effective when properly managed, requiring routine viral load monitoring to assess successful viral suppression. Efforts to expand access by decentralizing HIV nucleic acid testing in low- and middle-income countries (LMICs) has been hampered by the cost and complexity of current tests. Sample preparation of blood samples has traditionally relied on cumbersome RNA extraction methods, and it continues to be a key bottleneck for developing low-cost POC nucleic acid tests. We present a microfluidic paper-based analytical device (μPAD) for extracting RNA and detecting HIV in serum, leveraging low-cost materials, simple buffers, and an electric field. We detect HIV virions and MS2 bacteriophage internal control in human serum using a novel lysis and RNase inactivation method, paper-based isotachophoresis (ITP) for RNA extraction, and duplexed reverse transcription recombinase polymerase amplification (RT-RPA) for nucleic acid amplification. We design a specialized ITP system to extract and concentrate RNA, while excluding harsh reagents used for lysis and RNase inactivation. We found the ITP μPAD can extract and purify 5000 HIV RNA copies per mL of serum. We then demonstrate detection of HIV virions and MS2 bacteriophage in human serum within 45-minutes.

Online sample preconcentration techniques in nonaqueous capillary and microchip electrophoresis

One of the major drawbacks of electrophoresis in both capillary and microchip is the unsatisfactory sensitivity. Online sample preconcentration techniques can be regarded as the most common and powerful approaches commonly applied to enhance overall detection sensitivity. While the advances of various online preconcentration strategies in capillary and microchip employing aqueous background electrolytes are well-reviewed, there has been limited discussion of the feasible preconcentration techniques specifically developed for capillary and microchip using nonaqueous background electrolytes. This review provides the first consolidated overview of various online preconcentration techniques in nonaqueous capillary and microchip electrophoresis, covering the period of the last two decades. It covers developments in the field of sample stacking, isotachophoresis, and micellar-based stacking. Attention is also given to multi-stacking strategies that have been used for nonaqueous electrophoresis.

Microfluidic device for coupling isotachophoretic sample focusing with nanopore single-molecule sensing

Solid-state nanopores (NPs) are label-free single-molecule sensors, capable of performing highly sensitive assays from a small number of biomolecule translocation events. However, single-molecule sensing is challenging at extremely low analyte concentrations due to the limited flux of analytes to the sensing volume. This leads to a low event rate and increases the overall assay time. In this work, we present a method to enhance the event rate at low analyte concentrations by using isotachophoresis (ITP) to focus and deliver analytes to a nanopore sensor. Central to this method is a device capable of performing ITP focusing directly on a solid-state NP chip, while preventing the focusing electric field from damaging the nanopore membrane. We discuss considerations and trade-offs related to the design of the focusing channel, the ITP electrolyte system and electrical decoupling between the focusing and sensing modes. Finally, we demonstrate an integrated device wherein the concentration enhancement due to ITP focusing leads to an increase in event rate of >300-fold in the ITP-NP device as compared to the NP-only case.

Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer

We present an on-chip method for the extraction of RNA within a specific size range from low-abundance samples. We use isotachophoresis (ITP) with an ionic spacer and a sieving matrix to enable size-selection with a high yield of RNA in the target size range. The spacer zone separates two concentrated ITP peaks, the first containing unwanted single nucleotides and the second focusing RNA of the target size range (2-35 nt). Our ITP method excludes >90% of single nucleotides and >65% of longer RNAs (>35 nt). Compared to size selection using gel electrophoresis, ITP-based size-selection yields a 2.2-fold increase in the amount of extracted RNAs within the target size range. We also demonstrate compatibility of the ITP-based size-selection with downstream next generation sequencing. On-chip ITP-prepared samples reveal higher reproducibility of transcript-specific measurements compared to samples size-selected by gel electrophoresis. Our method offers an attractive alternative to conventional sample preparation for sequencing with shorter assay time, higher extraction efficiency and reproducibility. Potential applications of ITP-based size-selection include sequencing-based analyses of small RNAs from low-abundance samples such as rare cell types, samples from fluorescence activated cell sorting (FACS), or limited clinical samples.

Isotachophoresis applied to biomolecular reactions

This review discusses research developments and applications of isotachophoresis (ITP) to the initiation, control, and acceleration of chemical reactions, emphasizing reactions involving biomolecular reactants such as nucleic acids, proteins, and live cells. ITP is a versatile technique which requires no specific geometric design or material, and is compatible with a wide range of microfluidic and automated platforms. Though ITP has traditionally been used as a purification and separation technique, recent years have seen its emergence as a method to automate and speed up chemical reactions. ITP has been used to demonstrate up to 14 000-fold acceleration of nucleic acid assays, and has been used to enhance lateral flow and other immunoassays, and even whole bacterial cell detection assays. We here classify these studies into two categories: homogeneous (all reactants in solution) and heterogeneous (at least one reactant immobilized on a solid surface) assay configurations. For each category, we review and describe physical modeling and scaling of ITP-aided reaction assays, and elucidate key principles in ITP assay design. We summarize experimental advances, and identify common threads and approaches which researchers have used to optimize assay performance. Lastly, we propose unaddressed challenges and opportunities that could further improve these applications of ITP.

Capillary electrophoresis-based proteomic techniques for biomarker discovery

Besides proteome complexity, the greatest bioanalytical challenge facing comprehensive proteomic analysis, particularly in the identification of low abundance proteins, is related to the large variation of protein relative abundances. In contrast to universally enriching all analytes by a similar degree, the result of the capillary isotachophoresis (CITP) stacking process is that major components may be diluted, but trace compounds are concentrated. Such selective enhancement toward low abundance proteins drastically reduces the range of relative protein abundances within complex proteomes and greatly enhances the resulting proteome coverage. Furthermore, CITP offers seamless combination with nano-reversed phase liquid chromatography (nano-RPLC) as two highly resolving and completely orthogonal separation techniques critically needed for analyzing complex proteomes.

Limits of miniaturization: assessing ITP performance in sub-micron and nanochannels

The feasibility of isotachophoresis in channels of sub micrometer and nanometer dimension is investigated. A sample injection volume of 0.4 pL is focused and separated in a 330 nm deep channel. The sample consists of a biomatrix containing the fluorescently-labeled amino acids glutamate and phenylalanine, 20 attomoles of each. Isotachophoretic focusing is successfully demonstrated in a 50 nm deep channel. Separation of the two amino acids in the 50 nm deep channel however, could not be performed as the maximum applicable voltage was insufficient. This limit is imposed by bubble formation that we contribute to cavitation as a result of the mismatch in electro-osmotic flow, so called electrocavitation. This represents an unexpected limit on the miniaturization of ITP. Nonetheless, we report the smallest isotachophoretic separation and focusing experiment to date, both in terms of controlled sample injection volume and channel height.

[Evaluation of a new, microfluidic chip-based immunoassay for measurement of AFP-L3]

PURPOSE

AFP-L3 is an isoform of a-fetoprotein which has a fucosylated carbohydrate chain, and the fraction of AFP-L3/total AFP (AFP-L3%) specifically increases in hepatocellular carcinoma (HCC) patients and is widely used for screening and prognosis of HCC. The newly developed microTAS method which combines microchip electrophoresis and lectin affinity electrophoresis can rapidly provide AFP-L3% and total AFP measurements simultaneously at higher sensitivity. Here, we evaluated the system to know its analytical performance and clinical utility.

METHOD

Fully automated immunoanalyzer, microTASWako i30 which utilizes Liquid-phase Binding Assay-Electrokinetic Analyte Transport Assay (LBA-EATA method) as the assay principle was employed for the measurement of total AFP and AFP-L3%. We evaluated detection sensitivity, precision, accuracy, and correlation of the method.

RESULTS

The detection sensitivity was 0.3 ng/ml for both AFP-L1 and L3. The accuracy of the assay was 91.3-105.0% for total AFP. The precision of the assay was CV 1.9% at 2 ng/ml of total AFP, and CV 1.3% for 10% of AFP-L3% at 20ng/ml of total AFP. The microTAS method showed good correlation with the lectin affinity electrophoresis (AFP-L3 Test Wako) and the LBA methods (LBA Wako AFP-L3 on LiBASys) methods, giving correlation coefficient (r) of 0.988 and 0.988, respectively. The microTAS immunoreaction assay time and the total assay time including chip preparation were 1 and 9 min, respectively.

CONCLUSION

Since the microchip assay is rapid and highly sensitive, it should have better clinical utility than the current methods.

[Preconcentration and separation of DNA fragments based on microchip electrophoresis]

An online preconcentration method, electrokinetic supercharging (EKS) was used for the enrichment of DNA fragments based on microchip electrophoresis (MCE). EKS is a process that combines electrokinetic injection (EKI) with transient isotachophoresis (tITP). The results demonstrated that the large volume of low concentration sample could be introduced, preconcentrated, and eventually separated on a single channel microchip with the whole length of 40.5 mm. The limit of detection (S/N = 3) of DNA fragments was around 0.07 mg/L, effectively improved 40-fold by EKS preconcentration with the normal UV detection at 260 nm. Some important parameters for enhancing preconcentration and qualitative analysis were examined.