Utility of spermidine in PCR amplification of stool samples

Modern Approaches to de novo Synthesis of Extended DNA Fragments: Assembly of a Wide Repertoire of Sequences

The standardization of DNA fragment assembly methods for many tasks of synthetic biology is crucial. This is necessary for synthesizing a wider repertoire of sequences, as well as for further automation and miniaturization of such reactions. In this work, we proposed conditions for the assembly of DNA fragments from chemically synthesized oligonucleotides and we identified the errors occurring in the sequence under these conditions. Additionally, we proposed conditions for further combining synthetic fragments into larger DNA fragments. We showed that the optimized conditions are suitable for the assembly of a wide range of sequences.

PCR inhibitors and facilitators - Their role in forensic DNA analysis

Since its inception, DNA typing technology has been practiced as a robust tool in criminal investigations. Experts usually utilize STR profiles to identify and individualize the suspect. However, mtDNA and Y STR analyses are also considered in some sample-limiting conditions. Based on DNA profiles thus generated, forensic scientists often opine the results as Inclusion, exclusion, and inconclusive. Inclusion and exclusion were defined as concordant results; the inconclusive opinions create problems in conferring justice in a trial- since nothing concrete can be interpreted from the profile generated. The presence of inhibitor molecules in the sample is the primary factor behind these indefinite results. Recently, researchers have been emphasizing studying the sources of PCR inhibitors and their mechanism of inhibition. Furthermore, several mitigation strategies- to facilitate the DNA amplification reaction -have now found their place in the routine DNA typing assays with compromised biological samples. The present review paper attempts to provide a comprehensive review of PCR inhibitors, their source, mechanism of inhibition, and ways to mitigate their effect using PCR facilitators.

Optimization of reaction condition of recombinase polymerase amplification to detect SARS-CoV-2 DNA and RNA using a statistical method

Recombinase polymerase amplification (RPA) is an isothermal reaction that amplifies a target DNA sequence with a recombinase, a single-stranded DNA-binding protein (SSB), and a strand-displacing DNA polymerase. In this study, we optimized the reaction conditions of RPA to detect SARS-CoV-2 DNA and RNA using a statistical method to enhance the sensitivity. In vitro synthesized SARS-CoV-2 DNA and RNA were used as targets. After evaluating the concentration of each component, the uvsY, gp32, and ATP concentrations appeared to be rate-determining factors. In particular, the balance between the binding and dissociation of uvsX and DNA primer was precisely adjusted. Under the optimized condition, 60 copies of the target DNA were specifically detected. Detection of 60 copies of RNA was also achieved. Our results prove the fabrication flexibility of RPA reagents, leading to an expansion of the use of RPA in various fields.

New Developments in PCR-Based Diagnostics for Bacterial Pathogens Causing Gastrointestinal Infections-A Narrative Mini-Review on Challenges in the Tropics

The application of modern PCR approaches for the diagnosis of bacterial gastrointestinal pathogens is on the rise due to their rapidly available results combined with high sensitivity. While multiple studies describe the ongoing implementation of this technique for routine diagnostic purposes in laboratories in Western industrialized countries, reports on successful and also sustainable respective approaches in resource-poor tropical settings are still scarce. In order to shed light on potential reasons for this marked discrepancy, this narrative review summarizes identified challenges for the application of diagnostic PCR targeting bacterial gastrointestinal pathogens from stool samples in the tropics. The identified and discussed issues comprise the lack of generally accepted definitions for (1) minimum standards regarding sample acquisition, storage and transport time for diagnostic PCR analyses in the tropics, (2) nucleic acid extraction standards allowing an optimum detection of all types of pathogens which may be responsible for gastroenteritis in the tropics, (3) validation standards to ensure comparable quality of applied diagnostic assays, and (4) cut-offs for a reliable discrimination of infection and mere colonization in areas where semi-immunity due to repeated exposition associated with poor hygiene conditions has to be expected. Further implementation research is needed to solve those issues.

Ultrasensitive detection of protein biomarkers by MALDI-TOF mass spectrometry based on ZnFe2O4 nanoparticles and mass tagging signal amplification

A facile MALDI-TOF mass spectrometric platform for quantitative analysis of protein biomarkers was developed based on magnetic ZnFe₂O₄ nanoparticles and mass tagging signal amplification. In this platform, magnetic ZnFe₂O₄ nanoparticles functionalized with an aptamer of the biomarker of interest was used to magnetically separate silica nanoparticles modified with another aptamer of the target biomarker and a barcoding peptide from solution phase in the presence of the biomarker of interest. After the silica nanoparticles were dissolved by KHF₂, the released barcoding peptide was detected by MALDI-TOF mass spectrometry with magnetic ZnFe₂O₄ nanoparticles used as assisting matrix of laser desorption ionization. Since the mass spectral intensity of the barcoding peptide is directly related to the concentration of the target biomarker, the proposed platform can be applied to the quantification of the target biomarker in complex biological samples. The effectiveness of the proposed platform was tested on the detection of carcinoembryonic antigen (CEA) in serum. Experimental results revealed that the proposed platform could achieve quite reliable quantitative results for CEA in human serum samples with accuracy comparable to a commercial CEA ELISA Kit. Its limit of detection and limit of quantification for CEA were estimated to be 0.6 × 10^-3 and 1.8 × 10^-3 ng/mL, respectively, considerably lower than the corresponding values reported in literature. Due to its features of simplicity in design, extremely low background signal, high sensitivity and selectivity, the proposed method can be further developed to be a competitive alternative for the quantification of CEA and other protein biomarkers as well.

Alteration of enzymes and their application to nucleic acid amplification (Review)

Since the discovery of polymerase chain reaction (PCR) in 1985, several methods have been developed to achieve nucleic acid amplification, and are currently used in various fields including clinical diagnosis and life science research. Thus, a wealth of information has accumulated regarding nucleic acid-related enzymes. In this review, some nucleic acid-related enzymes were selected and the recent advances in their modification along with their application to nucleic acid amplification were described. The discussion also focused on optimization of the corresponding reaction conditions. Using newly developed enzymes under well-optimized reaction conditions, the sensitivity, specificity, and fidelity of nucleic acid tests can be improved successfully.

Improved amplification efficiency on stool samples by addition of spermidine and its use for non-invasive detection of colorectal cancer

Background

Using quantitative methylation-specific PCR (QM-MSP) is a promising method for colorectal cancer (CRC) diagnosis from stool samples. Difficulty in eliminating PCR inhibitors of this body fluid has been extensively reported. Here, spermidine is presented as PCR facilitator for the detection of stool DNA methylation biomarkers using QM-MSP. We examined its effectiveness with NPY, PENK and WIF1, three biomarkers which we have previously shown to be of relevance to CRC.

Results

We determined an optimal window for the amplification of the albumin (Alb) gene (100 ng of bisulfite-treated stool DNA added of 1 mM spermidine) at which we report that spermidine acts as a PCR facilitator (AE = 1680%) for SG RT-PCR. We show that the amplification of methylated PENK, NPY and WIF1 is considerably facilitated by QM-MSP as measured by an increase of CMI (Cumulative Methylation Index, i.e. the sum of the three methylation values) by a factor of 1.5 to 23 fold in individual samples, and of 10 fold in a pool of five samples.

Conclusions

We contend that spermidine greatly reduces the problems of PCR inhibition in stool samples. This observed feature, after validation on a larger sampling, could be used in the development of stool-based CRC diagnosis tests.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-015-0148-6) contains supplementary material, which is available to authorized users.