Amplification Process Research Articles

Generation and maintenance of the circularized multimeric IS26-associated translocatable unit encoding multidrug resistance

In gram-negative bacteria, IS26 often exists in multidrug resistance (MDR) regions, forming a pseudocompound transposon (PCTn) that can be tandemly amplified. It also generates a circular intermediate called the “translocatable unit (TU)”, but the TU has been detected only by PCR. Here, we demonstrate that in a Klebsiella pneumoniae MDR clone, mono- and multimeric forms of the TU were generated from the PCTn in a preexisting MDR plasmid where the inserted form of the TU was also tandemly amplified. The two modes of amplification were reproduced by culturing the original clone under antimicrobial selection pressure, and the amplified state was maintained in the absence of antibiotics. Mono- and multimeric forms of the circularized TU were generated in a RecA-dependent manner from the tandemly amplified TU, which can be generated in RecA-dependent and independent manners. These findings provide novel insights into the dynamic processes of genome amplification in bacteria.

Clinical evaluation of a novel digital microfluidic based point-of-care test platform for detection of SARS-Cov-2 and influenza A/B

Respiratory pathogens, such as SARS-CoV-2 and influenza A/B, can cause severe illnesses in susceptible individuals. This research evaluated a novel digital microfluidic point-of-care testing platform designed to detect 23 pathogens, comparing its performance to conventional laboratory-based nucleic acid tests. The platform integrates nucleic acid extraction and amplification processes for rapid detection with only 2 min of hands-on time. Performance assays demonstrated that the platform has high sensitivity (87 %-100 %) and specificity (99 %-100 %) for the detection of the evaluated 3 viruses. Additionally, the platform can be adapted for the detection of other respiratory pathogens, aiding in the early diagnosis of respiratory diseases, identifying the source of an outbreak or epidemic, and curbing the spread of the disease.

Real-time fluorescence loop-mediated isothermal amplification assays for detection of zoonotic malaria Plasmodium parasites

BackgroundNatural human infections by Plasmodium cynomolgi and P. inui have been reported recently and gain the substantial attention from Southeast Asian countries. Zoonotic transmission of non-human malaria parasites to humans from macaque monkeys occurred through the bites of the infected mosquitoes. The objective of this study is to establish real-time fluorescence loop-mediated isothermal amplification (LAMP) assays for the detection of zoonotic malaria parasites by combining real-time fluorescent technology with the isothermal amplification technique. MethodsBy using 18S rRNA as the target gene, the primers for P. cynomolgi, P. coatneyi and P. inui were newly designed in the present study. Four novel real-time fluorescence LAMP assays were developed for the detection of P. cynomolgi, P. coatneyi, P. inui and P. knowlesi. The entire amplification process was completed in 60 min, with the assays performed at 65 °C. By using SYTO-9 as the nucleic acid intercalating dye, the reaction was monitored via real-time fluorescence signal. ResultsThere was no observed cross-reactivity among the primers from different species. All 70 field-collected monkey samples were successfully amplified by real-time fluorescence LAMP assays. The detection limit for P. cynomolgi, P. coatneyi and P. knowlesi was 5 × 109 copies/µL. Meanwhile, the detection limit of P. inui was 5 × 1010 copies/µL. ConclusionThis is the first report of the detection of four zoonotic malaria parasites by real-time fluorescence LAMP approaches. It is an effective, rapid and simple-to-use technique. This presented platform exhibits considerable potential as an alternative detection for zoonotic malaria parasites.

A Foldable Thermoplastic Microdevice Integrating Isothermal Amplification and Schiff-Reaction-Based Colorimetric Assay for the Detection of Infectious Pathogens

In this study, we introduce a plastic-based foldable microdevice that integrates loop-mediated isothermal amplification (LAMP) and a colorimetric assay based on the Schiff reaction to detect the genes of infectious bacteria. The device comprises two sides: a sample zone containing amplification chambers and a detection zone for the colorimetric assay. The detection zone contains poly(methyl methacrylate) structures for transferring the colorimetric reagent-soaked glass micro-fiber paper into the sample chambers. Specific genes of Staphylococcus aureus (S. aureus) and Streptococcus pneumoniae (S. pneumoniae), the most common bacterial infection causes, were amplified by LAMP assay. The S. aureus gene was detected up to 10 fg/μL and the S. pneumoniae gene up to 0.1 pg/μL. The amplified target genes were visually identified using a colorimetric assay with Schiff’s reagent, which showed clear color discrimination through a reaction with aldehyde groups derived from the DNA in the amplicons. The introduced method, integrating amplification and detection processes in a single device, is expected to be utilized in point-of-care testing analysis for the simple and rapid detection of infectious pathogens.

Establishment and application of a rapid visual diagnostic method for Streptococcus agalactiae based on recombinase polymerase amplification and lateral flow strips

This study aims to establish a rapid diagnostic method for Streptococcus agalactiae (GBS) based on recombinase polymerase amplification (RPA) and lateral flow strips (LFS). The best primer pairs designed by SIP gene were screened according to the basic RPA reaction, then the probe was designed. The reaction condition was optimized based on the color development of the LFS detection line. To ascertain the reaction specificity, 10 common clinical pathogens and 10 clinical specimens of GBS were tested. Furthermore, the reaction sensitivity was assessed by utilizing a tenfold gradient dilution of GBS genomic DNA as templates. RPA–LFS method was compared to the qPCR assay and biochemical culture method for the Kappa consistency test. The RPA–LFS technique was able to complete the amplification process within 30 min and the results were observed on lateral flow strips. The method is highly sensitive, with a minimum detection limit of 1.31 ng for GBS. The RPA–LFS method showed consistent accuracy of results compared to qPCR and the culture–biochemical method. The establishment of this method is conducive to the development of on-site immediate detection, which can provide information for the timely development of a reasonable antimicrobial treatment plan, and has a greater potential for clinical application.

Aptamer-based protein molecule detection via cyclic reverse transcription coupling with self-priming hairpin-triggered CRISPR-Cas12a system

Protein biomarkers (e.g. thrombin) are of great significance for the biological process of the organism, and its aberrant expression is closely associated with the development of diseases. With thrombin, a serine protease that plays a crucial role in maintaining homeostasis and promoting blood clotting, as detection target, this study introduces a novel approach for sensitive and accurate measurement of protein biomarker expression by utilization of cyclic reverse transcription (CRT) in combination with the self-priming hairpin-triggered CRISPR-Cas12a system. In this method, an elegantly designed sensing probe is utilized to specifically bind with the thrombin protein and convert the protein signals to nucleic acids signals, following by the CRT and CRISPR-Cas12a system-based signal amplification strategy. Taking the merit of the two-stage amplification, this assay has the capability to detect thrombin at the fM level. In addition, due to the aptamer sequence’s strong selectivity to thrombin protein and the dual-check process in the signal amplification process (first in the CRT and second in the CRISPR system), the proposed test demonstrates exceptional specificity in detecting thrombin. By re-designing the sensing probe, the established method could be extended to various protein biomarker detection. Ultimately, this assay has successfully enabled the accurate evaluation of biomarker levels in constructed clinical samples, showing significant potential for application in the realm of clinical molecular diagnosis.

Bottom’s Dream and the Amplification of Filamentary Gas Structures and Stellar Spiral Arms

Abstract Theories of spiral structure traditionally separate into tight-winding Lin–Shu spiral density waves and the swing-amplified material patterns of Goldreich & Lynden-Bell and Julian & Toomre. In this paper we consolidate these two types of spirals into a unified description, treating density waves beyond the tight-winding limit, in the regime of shearing and nonsteady open spirals. This shearing wave scenario novelly captures swing amplification that enables structure formation above conventional Q thresholds. However, it also highlights the fundamental role of spiral forcing on the amplification process in general, whether the wave is shearing or not. Thus it captures resonant and nonresonant mode growth through the donkey effect described by Lynden-Bell & Kalnajs and, critically, the cessation of growth when donkey behavior is no longer permitted. Our calculations predict growth exclusive to trailing spirals above the Jeans length, the prominence of spirals across a range of orientations that increases with decreasing arm multiplicity, and a critical orientation where growth is fastest that is the same for both modes and material patterns. Predicted structures are consistent with highly regular, high-multiplicity gaseous spur features and long filaments spaced close to the Jeans scale in spirals and bars. Applied to stellar disks, conditions favor low multiplicity (m < 5) open trailing spirals with pitch angles in the observed range 10° < i p < 50°. The results of this work serve as a basis for describing spirals as a unified class of transient waves, abundantly stimulated but narrowly selected for growth depending on local conditions.

Tuning the Dynamic Reaction Balance of CRISPR/Cas12a and RPA in One Pot: A Key to Switch Nucleic Acid Quantification.

Excavating nucleic acid quantitative capabilities by combining clustered regularly interspaced short palindromic repeats (CRISPR) and isothermal amplification in one pot is of common interest. However, the mutual interference between CRISPR cleavage and isothermal amplification is the primary obstacle to quantitative detection. Though several works have demonstrated enhanced detection sensitivity by reducing the inhibition of CRISPR on amplification in one pot, few paid attention to the amplification process and even dynamic reaction processes between the two. Herein, we find that DNA quantification can be realized by regulating either recombinase polymerase amplification (RPA) efficiency or CRISPR/Cas12a cleaving efficiency (namely, tuning the dynamic reaction balance) in one pot. The sensitive quantification is realized by utilizing dual PAM-free crRNAs for CRISPR/Cas12a recognition. The varied RPA primer concentration with stabilized CRISPR systems significantly affects the amplification efficiency and quantitative performances. Alternatively, quantitative detection can also be achieved by stabilizing the amplification process while regulating the CRISPR/Cas12a concentration. The quantitative capability is proved by detecting DNA targets from Lactobacillus acetotolerans and SARS-CoV-2. The quantitative performance toward real samples is comparable to quantitative real-time PCR for detecting L. acetotolerans spiked in fermented food samples and SARS-CoV-2 clinical samples. We expect that the presented method will be a powerful tool for quantifying other nucleic acid targets.

Purification of DNA Nanoparticles Using Photocleavable Biotin Tethers.

The number of applications of self-assembled deoxyribonucleic acid (DNA) origami nanoparticles (DNA NPs) has increased drastically, following the development of a variety of single-stranded template DNA (ssDNA) that can serve as the scaffold strand. In addition to viral genomes, such as M13 bacteriophage and lambda DNAs, enzymatically produced ssDNA from various template sources is rapidly gaining traction and being applied as the scaffold for DNA NP preparation. However, separating fully formed DNA NPs that have custom scaffolds from crude assembly mixes is often a multistep process of first separating the ssDNA scaffold from its enzymatic amplification process and then isolating the assembled DNA NPs from excess precursor strands. Only then is the DNA NP sample ready for downstream characterization and application. In this work, we highlight a single-step purification of custom sequence- or M13-derived scaffold-based DNA NPs using photocleavable biotin tethers. The process only requires an inexpensive ultraviolet (UV) lamp, and DNA NPs with up to 90% yield and high purity are obtained. We show the versatility of the process in separating two multihelix bundle structures and a wireframe polyhedral architecture.

A split single-stranded DNA activator-based Cas12a fluorescence biosensor for specific H1N1 detection

We developed a novel CRISPR/Cas12a fluorescence biosensor to specifically detect the H1N1 virus based on splitting single-stranded DNA (ssDNA) activators. Specifically, activators 1 and 2 were generated from dual target nucleic acid sites to induce a three-way junction (3WJ) isothermal amplification process. Two specific H1N1 RNA nucleic acid sites were bound to a set of probes to form a 3WJ, which facilitated repeated extension and nicking reactions to produce high levels of split ssDNA activators via DNA polymerase and nicking endonuclease activity. Amplified activators 1 and 2 fully assembled with Cas12a/crRNA to form complexes. Activated Cas12a trans-cleaved ssDNA reporter molecules to generate fluorescence signals. Under optimal conditions, biosensor dynamic detection range was 1 pM–10 nM, and the detection limit was 205 fM. Thus, our biosensor showed high specificity, reliability, and robustness, which highlights its potential use for H1N1 diagnostics.

A triple-amplified electrochemical-photoelectrochemical dual-mode biosensing platform for viral gene assay based on catalytic hairpin assembly, CRISPR-Cas12a and liposome-entrapped bifunctional methylene blue

Taking SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) gene as the model due to the great destructiveness of COVID-19 in the past years, a triple-amplified electrochemical-photoelectrochemical (EC-PEC) dual-mode biosensing platform was constructed for viral gene assay based on catalytic hairpin assembly (CHA), CRISPR-Cas12a and liposome-entrapped bifunctional methylene blue. Firstly, the SARS-CoV-2 RdRp gene triggered CHA nonenzymatic amplification process to produce large amounts of double-stranded DNA (dsDNA) that could activate CRISPR-Cas12a trans-cleavage ability. Subsequently, the activated CRISPR-Cas12a trans-cleaved nearby ssDNA carrying methylene blue (MB)-encapsulated liposome sphere (MELS) and streptavidin-modified magnetic bead (SMB), and lots of MELS were released. After magnetic separation, MELS was lysed by Triton X-100, releasing a large quantity of bifunctional MB molecules that not only generate an obvious EC signal originated from the electro-oxidation of MB, but also effectively induce the photocurrent-polarity-switching of the Sb2S3 NRs-modified photoelectrode from cathodic photocurrent to anodic photocurrent and generate a large anodic photocurrent. Based on the combination of the above triple amplification processes with MB-induced photocurrent-polarity-switching and EC-PEC dual-mode sensing strategies, the SARS CoV-2 RdRp gene was sensitively, selectively and accurately assayed with a linear response range of 0.1 fM – 10nM (1 aM – 10nM) and a detection limit of 69.6 aM (0.11 aM) for EC (PEC) method. The proposed EC-PEC dual-mode biosensor is also easily extended to the analysis of other viral nucleic acid by changing the related sequences of H1 and H2 DNAs, providing a new way in the early diagnosis and epidemic control of diseases caused by viruses.

Quantum dueling: an efficient solution for combinatorial optimization

In this paper, we present a new algorithm for generic combinatorial optimization, which we term quantum dueling. Traditionally, potential solutions to the given optimization problems were encoded in a ‘register’ of qubits. Various techniques are used to increase the probability of finding the best solution upon measurement. Quantum dueling innovates by integrating an additional qubit register, effectively creating a ‘dueling’ scenario where two sets of solutions compete. This dual-register setup allows for a dynamic amplification process: in each iteration, one register is designated as the ‘opponent,’ against which the other register’s more favorable solutions are enhanced through a controlled quantum search. This iterative process gradually steers the quantum state within both registers toward the optimal solution. With a quantitative contraction for the evolution of the state vector, classical simulation under a broad range of scenarios and hyper-parameter selection schemes shows that a quadratic speedup is achieved, which is further tested in more real-world situations. In addition, quantum dueling can be generalized to incorporate arbitrary quantum search techniques and as a quantum subroutine within a higher-level algorithm. Our work demonstrates that increasing the number of qubits allows the development of previously unthought-of algorithms, paving the way for advancement of efficient quantum algorithm design.

Development and Application of a Duplex RT-RPA Assay for the Simultaneous Detection of Cymbidium mosaic virus and Odontoglossum ringspot virus.

Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) are among the world's most serious and widespread orchid viruses; they often infect orchids, causing devastating losses to the orchid industry. Therefore, it is critical to establish a method that can rapidly and accurately detect viruses in the field using simple instruments, which will largely reduce the further spread of viruses and improve the quality of the orchid industry and is suitable for mass promotion and application at grassroots agrotechnical service points. In this investigation, we established a rapid amplification method for virus detection at 39 °C for 35 min to detect the presence of CymMV and ORSV simultaneously, sensitively, and specifically in orchids. Primers for the capsid protein (CP)-encoding genes of both viruses were designed and screened, and the reaction conditions were optimized. The experimental amplification process was completed in just 35 min at 39 °C. There were no instances of nonspecific amplification observed when nine other viruses were present. The RPA approach had detection limits of 104 and 103 copies for pMD19T-CymMV and pMD19T-ORSV, respectively. Moreover, the duplex RT-RPA investigation confirmed sensitivity and accuracy via a comparison of detection results from 20 field samples with those of a gene chip. This study presents a precise and reliable detection method for CymMV and ORSV using RT-RPA. The results demonstrate the potential of this method for rapid virus detection. It is evident that this method could have practical applications in virus detection processes.

Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography.

The detection of multiple single nucleotide polymorphisms (SNPs) of circulating tumor DNA (ctDNA) is still a great challenge. In this study, we designed enzyme-assisted nucleic acid strand displacement amplification combined with high-performance liquid chromatography (HPLC) for the simultaneous detection of three ctDNA SNPs. First, the trace ctDNA could be hybridized to the specially designed template strand, which initiated the strand displacement nucleic acid amplification process under the synergistic action of DNA polymerase and restriction endonuclease. Then, the targets would be replaced with G-quadruplex fluorescent probes with different tail lengths. Finally, the HPLC-fluorescence assay enabled the separation and quantification of multiple signals. Notably, this method can simultaneously detect both the wild type (WT) and mutant type (MT) of multiple ctDNA SNPs. Within a linear range of 0.1 fM-0.1 nM, the detection limits of BRAF V600E-WT, EGFR T790M-WT, and KRAS 134A-WT and BRAF V600E-MT, EGFR T790M-MT, and KRAS 134A-MT were 29, 31, and 11 aM and 22, 29, and 33 aM, respectively. By using this method, the mutation rates of multiple ctDNA SNPs in blood samples from patients with lung or breast cancer can be obtained in a simple way, providing a convenient and highly sensitive analytical assay for the early screening and monitoring of lung cancer.

Abstract 5188: Defining PD-1/PD-L1 receptor-ligand interactions in the head and neck cancer tumor microenvironment identifies unique ‘immune cell rivers’ of cellular interactions

Abstract Head and neck squamous cell carcinoma (HNSCC) is the 7th most common cancer globally with a poor 5-year survival rate of ~50%. With the emerging successes with immune checkpoint blockade (ICB) in the metastatic and recurrent setting, there is a need for predictive biomarkers to identify patients likely to achieve clinical benefit. Whilst PD-L1 expression on tumour cells and PD-1 on immune cells have been investigated, these remain inconclusive biomarkers. To better understand and map the PD-L1/PD-1 receptor-ligand interactions, we evaluated a novel in situ proximity ligation assay (is PLA) across whole tissue sections of pre-treatment HNSCC patients to received ICB therapy. Pre-treatment FFPE whole tissue samples were collected from n=25 advanced stage HNSCC patients across two major Queensland Hospitals (Royal Brisbane and Women’s Hospital and the Princess Alexandra Hospital). Tissues were stained with multiplex immunofluorescence and the Navinci Diagnostics fluorescent is PLA assay for PD-1/PD-L1. Tissues were incubated with the PD1/PD-L1 antibodies and subsequent incubation with oligonucleotide-tagged secondary probes enabled PLA, which highlights PD1 and PD-L1 interactions. Following the application of secondary probes, the sections underwent a ligation step, then a post-blocking, and an amplification process to enhance the detection of protein interactions. Next, the sections were treated with a detection solution to visualize the amplification product. The PLA assay findings were measured against clinical endpoints (PFS/OS criteria). In n=5/25 HNSCC tissues, positive PD-1/PD-L1 interactions were measured across the tumour microenvironment (TME), specifically in the immune rivers on the immediate tumour periphery. These cells showed highly specific binding of the PLA product. These areas positive by the PLA assay were in stark contrast to the tumour bulk/nests which were absent in PD-1/PD-L1 interactions. Notably, the PLA PD-1/PD-L1 do not correlate with tumour PD-L1 expression or tumour proportion scores (TPS). Rather, our study highlighted the difference in spatially mapping PD-1/PD-L1 interactions which may better recapitulate the tumour-immune recognition and activity in the TME. Taken together, these data provide a novel approach for determining clinically relevant receptor/ligand interactions in the HNSCC TME. Citation Format: Habib Sadeghirad, Vahid Yaghoubi Naei, James Monkman, Subham Basu, Agata Wicher, Rahul Ladwa, Brett GM Hughes, Arutha Kulasinghe. Defining PD-1/PD-L1 receptor-ligand interactions in the head and neck cancer tumor microenvironment identifies unique ‘immune cell rivers’ of cellular interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5188.

CRISPR-Cas9-guided amplification-free genomic diagnosis for familial hypercholesterolemia using nanopore sequencing.

Familial hypercholesterolemia is an inherited disorder that remains underdiagnosed. Conventional genetic testing methods such as next-generation sequencing (NGS) or target PCR are based on the amplification process. Due to the efficiency limits of polymerase and ligase enzymes, these methods usually target short regions and do not detect large mutations straightforwardly. This study combined the long-read nanopore sequencing and CRISPR-Cas9 system to sequence the target DNA molecules without amplification. We originally designed and optimized the CRISPR-RNA panel to target the low-density lipoprotein receptor gene (LDLR) and proprotein convertase subtilisin/kexin type 9 gene (PCSK9) from human genomic DNA followed by nanopore sequencing. The average coverages for LDLR and PCSK9 were 106× and 420×, versus 1.2× for the background genome. Among them, continuous reads were 52x and 307x, respectively, and spanned the entire length of LDLR and PCSK9. We identified pathogenic mutations in both coding and splicing donor regions in LDLR. We also detected an 11,029 bp large deletion in another case. Furthermore, using continuous long reads generated from the benchmark experiment, we demonstrated how a false-positive 670 bp deletion caused by PCR amplification errors was easily eliminated.

A sensitive one-pot ROA assay for rapid miRNA detection

MicroRNAs (miRNAs) and short RNA fragments (18–25 nt) are crucial biomarkers in biological research and disease diagnostics. However, their accurate and rapid detection remains a challenge, largely due to their low abundance, short length, and sequence similarities. In this study, we report on a highly sensitive, one-step RNA O-circle amplification (ROA) assay for rapid and accurate miRNA detection. The ROA assay commences with the hybridization of a circular probe with the test RNA, followed by a linear rolling circle amplification (RCA) using dUTP. This amplification process is facilitated by U-nick reactions, which lead to an exponential amplification for readout. Under optimized conditions, assays can be completed within an hour, producing an amplification yield up to the microgram level, with a detection limit as low as 0.15 fmol (6 pM). Notably, the ROA assay requires only one step, and the results can be easily read visually, making it user-friendly. This ROA assay has proven effective in detecting various miRNAs and phage ssRNA. Overall, the ROA assay offers a user-friendly, rapid, and accurate solution for miRNA detection.

Dispersion‐Engineered Super‐Gain Parametric Amplification in Nanoscale Optical Cavities

The gain factor of the optical parametric amplification (OPA) process is known to be negligible in the small scale due to low‐interaction‐medium length. Hence, in the nanoscale, OPA is deemed as infeasible. Therefore, in small‐scale‐integrated optical devices, stimulated‐emission‐based amplifiers (lasers) are employed instead of OPAs. In contrast, the major advantage of OPAs over lasers is that unlike lasers which only provide amplification over a narrow spectral band, OPAs provide high‐gain amplification over a very large, user‐controlled spectral band. In this article, it is shown that OPA can yield wideband high‐gain amplification over a nanoscale beam propagation distance through dispersion engineering. This is achieved by a proper tuning of the pump (source) wave frequency, which can maximize the effective medium nonlinearity by a few orders of magnitude, while concurrently maximizing the intracavity energy density, thereby compensating for the small co‐propagation distance for the input (signal) and pump beams. In this study, it is shown that an input wave can be amplified by a factor in a nanoscale cavity via precise dispersion engineering. Both empirical and computational formulations are used for the investigation, which display a reasonable agreement.

Direct TAMRA-dUTP labeling of M. tuberculosis genes using loop-mediated isothermal amplification (LAMP)

Fluorescent molecule-based direct labeling of amplified DNA is a sensitive method employed across diverse DNA detection and diagnostics systems. However, using pre-labeled primers only allows for the attachment of a single fluorophore to each DNA strand and any modifications of the system are less flexible, requiring new sets of primers. As an alternative, direct labeling of amplified products with modified nucleotides is available, but still poorly characterized. To address these limitations, we sought a direct and adaptable approach to label amplicons produced through Loop-mediated isothermal amplification (LAMP), using labeled nucleotides (dUTPs) rather than primers. The focus of this study was the development and examination of a direct labeling technique of specific genes, including those associated with drug resistance in Mycobacterium tuberculosis. We used 5-(3-Aminoallyl)-2′-deoxyuridine-5′triphosphate, tagged with 5/6-TAMRA (TAMRA-dUTP) for labeling LAMP amplicons during the amplification process and characterized amplification and incorporation efficiency. The optimal TAMRA-dUTP concentration was first determined based on amplification efficiency (0.5% to total dNTPs). Higher concentrations of modified nucleotides reduced or completely inhibited the amplification yield. Target size also showed to be determinant to the success of amplification, as longer sequences showed lower amplification rates, thus less TAMRA incorporated amplicons. Finally, we were able to successfully amplify all four M. tuberculosis target genes using LAMP and TAMRA-modified dUTPs.

Robust multi-read reconstruction from noisy clusters using deep neural network for DNA storage

DNA holds immense potential as an emerging data storage medium. However, the recovery of information in DNA storage systems faces challenges posed by various errors, including IDS errors, strand breaks, and rearrangements, inevitably introduced during synthesis, amplification, sequencing, and storage processes. Sequence reconstruction, crucial for decoding, involves inferring the DNA reference from a cluster of erroneous copies. While most methods assume equal contributions from all reads within a cluster as noisy copies of the same reference, they often overlook the existence of contaminated sequences caused by DNA breaks, rearrangements, or mis-clustering reads. To address this issue, we propose RobuSeqNet, a robust multi-read reconstruction neural network specifically designed to robustly reconstruct multiple reads, accommodating noisy clusters with strand breakage, rearrangements, and mis-clustered strands. Leveraging the attention mechanism and an elaborate network design, RobuSeqNet exhibits resilience to highly-noisy clusters and effectively deals with in-strand IDS errors. The effectiveness and robustness of the proposed method are validated on three representative next-generation sequencing datasets. Results demonstrate that RobuSeqNet maintains high sequence reconstruction success rates of 99.74%, 99.58%, and 96.44% across three datasets, even in the presence of noisy clusters containing up to 20% contaminated sequences, outperforming known sequence reconstruction models. Additionally, in scenarios without contaminated sequences, it exhibits comparable performance to existing models, achieving success rates of 99.88%, 99.82%, and 97.68% across the three datasets.