Real-time fluorescence ligase chain reaction for sensitive detection of single nucleotide polymorphism based on fluorescence resonance energy transfer

Sun, Yueying; Lü, Xiaohui; Su, Fengxia; Wang, Limei; Liu, Chenghui; Duan, Xinrui; Li, Zhengping

doi:10.1016/j.bios.2015.07.028

Cited by 34 publications

(19 citation statements)

References 32 publications

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“…While there have been studies which have reported the use of ligation reaction for point mutation detection, this study is unique in its integration of both quantum dots and magnetic nanoparticles in LDR-PCR free system. [47][48][49] Meng and Battistella described a convenient genotyping method capable of detecting point mutations directly in human genomic DNA based on the combination of ligase chain reaction (LCR) and microbead-enrichment technique. LCR probes, including a biotin-labelled common probe and two uorescence-labelled allele-specic probes, were designed for two alleles of a mutated site.…”

Section: Discussionmentioning

confidence: 99%

Fluorescent detection of point mutation via ligase reaction assisted by quantum dots and magnetic nanoparticle-based probes

2017

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Section: Discussionmentioning

confidence: 99%

Fluorescent detection of point mutation via ligase reaction assisted by quantum dots and magnetic nanoparticle-based probes

2017

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“…However, the SMAP2 technology requires complicated design of primers, special DNA polymerase and MutS protein . More recently, our group has developed one‐step SNP detection with real‐time fluorescence ligase chain reaction (LCR), but this method needs doubly labeled DNA probes and precise thermal cycling similar to PCR …”

Section: Methodsmentioning

confidence: 99%

One‐Step Quantitative Single Nucleotide Polymorphism (SNP) Diagnosis By Modified Loop‐Mediated Isothermal Amplification (mLAMP)

Ren

Duan

et al. 2019

ChemistrySelect

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Single nucleotide polymorphism (SNP) detection usually needs two steps: amplification (mostly by polymerase chain reaction) and genotyping of SNP by using the amplification products. To shorten the time and simplify the detection, it is ideal to develop a one-step method, in which the amplification itself can be the SNP detection signal. Meanwhile the difficulty in developing one-step technology is the suppression of the background amplification. In this work, we designed an artificial mismatch into the third position from the 3' terminus of the probes to prevent false positive extension reaction of the probes, which greatly improved the selectivity of mutation detection. We integrated this high selective version of primer extension reaction with a rapid and isothermal nucleic acid amplification loop-mediated isothermal amplification (LAMP) method to distinguish between wild-type and mutant DNA. SYBR ® Green I is selected as the fluorescent dye that is tested for real-time measurement of the LAMP reaction by its fluorescence intensity.100aM single strand DNA (ssDNA) or double strand DNA (dsDNA) targets can be accurately determined and as low as 0.1% mutant DNA can be detected in the presence of a large excess of wild-type DNA, indicating the high sensitivity and specificity. The real-time measuring does not require the detection step after LAMP and gives a wide dynamic range for detection of DNA targets (from 100aM to 1 pM).Single nucleotide polymorphisms (SNPs) are the most frequent type of variation in the human genome, which are single nucleotide change with an estimated frequency of one to two polymorphic nucleotides per kilobase. [1] They can be used as not only high-resolution genetic markers for mapping gene, defining population structure, and performing gene association studies but also a fundamental tool for drug discovery and identification of numerous genetic diseases. [2] SNP detection generally needs two steps: amplification of target DNA and genotyping of SNP by using the amplification products. [3] Amplification, usually by the polymerase chain reaction (PCR), is a powerful tool to achieve enough sensitivity for detection of genomic DNA. In principle, the allele-specific PCR, by designing a primer with the nucleotide at its 3'-end complementary to the base at the SNP site in the detected targets, can directly detect SNP. However, the DNA polymerase cannot provide enough specificity to accurately discriminate single-base mis-match. The mismatched primer extension often occurs and the extension products can subsequently be exponentially amplified with PCR prone to generate of false positive results. [4] Therefore, the genomic DNA region that spans the SNP sites of interest needed to be amplified by PCR, and then the amplification products were genotyped at the SNP sites by using allele-specific hybridization, oligonucleic ligation, [5] invasive cleavage, [6] primer extension, and so on, [7] The padlock probes can be specifically ligated with DNA ligase when they are perfectly complementary to the DN...

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“…The latter was resistant to exonuclease I and exonuclease III degradation. Sun et al developed a robust real-time based LCR for p53 SNP (Arg282Trp) genotyping [110]. In this assay, two probes were used.…”

Section: Fluorescence Resonance Energy Transfer (Fret)mentioning

confidence: 99%

“…Limitations in multiplexing potential and high-throughput along with high background signal due to target independent ligation, especially in absence of target DNA, were the main drawbacks for conventional LCR [48,49,154]. The conventional method requires a conventional thermal cycler with either an autoradiography, spectrophotometric or fluorometric detection method [99][100][101][102][103][104]110,111]. Electrochemical detection was recently enabled with conventional LCR through the use of microdevices and a potentiostat with 3 electrode system [115,116].…”

Section: Comparative Evaluation For Various Versions Of Lcr and Ligatmentioning

confidence: 99%

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Gibriel

Adel

2017

Mutation Research/Reviews in Mutation Research

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Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.

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Real-time fluorescence ligase chain reaction for sensitive detection of single nucleotide polymorphism based on fluorescence resonance energy transfer

Cited by 34 publications

References 32 publications

Fluorescent detection of point mutation via ligase reaction assisted by quantum dots and magnetic nanoparticle-based probes

Fluorescent detection of point mutation via ligase reaction assisted by quantum dots and magnetic nanoparticle-based probes

One‐Step Quantitative Single Nucleotide Polymorphism (SNP) Diagnosis By Modified Loop‐Mediated Isothermal Amplification (mLAMP)

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

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