Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants

Liu, Weipeng; Zhu, Minjun; Liu, Hongxing; Wei, Jitao; Zhou, Xiaoming; Xing, Da

doi:10.1016/j.bios.2016.02.073

Cited by 21 publications

(6 citation statements)

References 36 publications

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“…In another approach, RNA target molecules were used to trigger the formation of a Au-NP containing DNA network for colorimetric readout, which facilitated differentation between the 16S rRNAs of closely related bacteria with a detection limit of ≥5 × 10 5 CFU . Similar as for the HCR and CHA discussed above, also a large number of miRNA sensors have been developed (Figure ), which utilize strand displacement reactions in their sensing scheme, achieving detection of miRNA from the nanomolar down to the femtomolar range. ,− Of note, Zhang et al achieved detection of miRNA at a concentration of 67 aM using a DNA walker scheme, and Shen et al also used strand displacement techniques for sensitive miRNA imaging …”

Section: Applications In Sensing Diagnostics and Therapeuticsmentioning

confidence: 99%

Principles and Applications of Nucleic Acid Strand Displacement Reactions

2019

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Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNAbased nanomachine et al. Nature 2000, 406, 605−608). Since then, toeholdmediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287−294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

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Section: Applications In Sensing Diagnostics and Therapeuticsmentioning

confidence: 99%

Principles and Applications of Nucleic Acid Strand Displacement Reactions

2019

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“…We speculate that this exceptionally high discrimination for C > X and G > X mutation can be attributed to a large energy barrier with the replacement of a C–G pair with a mismatch in the assay of the wild-type. In summary, our system provides remarkable DF ranging from 57 to absolute discrimination with a median of 491, which is comparable with some recently reported methods. ,, …”

Section: Resultsmentioning

confidence: 99%

“…In summary, our system provides remarkable DF ranging from 57 to absolute discrimination with a median of 491, which is comparable with some recently reported methods. 16,37,38 Detection of Single Nucleotide Mutation at Low Abundance and Mutation Detection in Cancer Cell Line.…”

Section: Acs Sensorsmentioning

confidence: 99%

Discrimination Cascade Enabled Selective Detection of Single-Nucleotide Mutation

Xiao

et al. 2017

ACS Sens.

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Owing to the significance of single nucleotide mutation (SNM) for personalized medicine, the detection of SNM with high accuracy has recently attracted considerable interest. Here, we present a kinetic method for selective detection of SNM based on a discrimination cascade constructed by combining the toehold strand displacement (TSD) and endonuclease IV (Endo IV) catalyzed hydrolysis. The single-nucleotide specificity of the two DNA reactions allows highly selective detection of all types of single nucleotide changes (including single-nucleotide insertion and deletion), achieving a high discrimination factor with a median of 491 which is comparable with recently reported methods. For the first time, the enzyme assisted nucleic acid assay was characterized by single molecule analysis on total internal reflection fluorescence microscope (TIRFM) suggesting that the two steps do not work independently and the rate of TSD can be tuned by Endo IV facilitated conformation selection. The effective discrimination of the point mutation of BRAF gene in cancer and normal cell line suggests that this method can be a prominent post-PCR genotyping assay.

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“…As one kind of strand displacement amplification reaction (SDA), ISAR would be applied to transform one miRNA into plenty of DNAs for activating the collateral trans-cleavage nuclease activity of Cas12a, which can be activated only by the recognition of DNA. ISAR could obtain more DNA products for sensitive detection of miRNA at constant temperature and effectively bypass the requirement of the thermal cycler. , ISAR was based on continuous stack hybridization and toehold exchange reactions and functions by changing the hybridization position of the primers. So, we utilized the OSCC-associated miRNA-mediated ISAR/Cas12a strategy to realize cascade synergistic cyclic amplification.…”

Section: Introductionmentioning

confidence: 99%

“…ISAR could obtain more DNA products for sensitive detection of miRNA at constant temperature and effectively bypass the requirement of the thermal cycler. 22,23 ISAR was based on continuous stack hybridization and toehold exchange reactions and functions by changing the hybridization position of the primers. So, we utilized the OSCCassociated miRNA-mediated ISAR/Cas12a strategy to realize cascade synergistic cyclic amplification.…”

Section: Introductionmentioning

confidence: 99%

Paper-Based Strip for Ultrasensitive Detection of OSCC-Associated Salivary MicroRNA via CRISPR/Cas12a Coupling with IS-Primer Amplification Reaction

Chen

Luo

et al. 2020

Anal. Chem.

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As the most common malignancy in humans, oral squamous cell carcinoma (OSCC) not only harms the people's health but also undermines their confidence after facial surgery. Early detection and treatment can effectively reduce these damages. The unique collateral trans-cleavage nuclease activity of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system was utilized to realize the detection of nucleic acid with high sensitivity. So, in this work, we designed a point-of-care testing (POCT) platform for the detection of OSCC-associated salivary hsa-miRNA 31-5p (miR-31) via the cascade signal amplification of "invading stacking primer" (IS-primer) amplification reaction (ISAR), CRISPR/Cas12a, and dual-mode paper-based strip (dm-Strip). To amplify the detection signal of trace miR-31, the cascade signal amplification of CRISPR/Cas12a system coupling with ISAR was designed in a one-pot reaction at a constant temperature. The target miR-31 could activate the ISAR to generate numerous DNAs, which would further trigger the trans-cleavage effect of Cas12a to catalyze the nonspecific single-stranded DNA (ssDNA) cleavage. This ssDNA was labeled with digoxin and biotin at the 5′ and 3′ termini (digoxin/ssDNA/biotin), respectively, which led to generate the naked-eye signal and fluorescent signal of the designed dm-Strip. The whole detection time was 90 min with limit-of-detection (LOD) down to aM level. This ISAR/Cas12abased dm-Strip (ISAR/Cas12a-dmStrip) allowed for the portable and ultrasensitive detection of miRNA, an important step in early diagnosis of OSCC and biomedical research. Recent studies indicated that miR-31 was validated as an upregulated biomarker in saliva for OSCC. 8 Accurate and sensitive quantification of salivary miR-31 could contribute to the easier medical screening of OSCC in underserved communities and modify the outcome of OSCC. 9,10 Toward these needs, a sensitive and portable sensor is urgently in demand to quantify salivary miR-31 for the early diagnosis and effective monitoring of OSCC in underserved communities.Recent advances of CRISPR-associated (CRISPR/Cas) systems were applied to construct detection methods. 11−14 The unique collateral trans-cleavage nuclease activity of the Cas12a system was utilized to realize the detection of nucleic acid with high sensitivity and specificity. 15−17 The collateral DNase activity of Cas12a can be switched on by the target DNA, which usually helps ultrasensitive detection of DNA. 11,18,19 Unlike Cas13a, both the target and probe of Cas12a are DNA, which improves the stability of the detection assay and reduces costing significantly. 15,20 Therefore, utilizing Cas12a for the detection of miRNA would be more reliable

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Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants

Cited by 21 publications

References 36 publications

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Discrimination Cascade Enabled Selective Detection of Single-Nucleotide Mutation

Paper-Based Strip for Ultrasensitive Detection of OSCC-Associated Salivary MicroRNA via CRISPR/Cas12a Coupling with IS-Primer Amplification Reaction

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