scholarly journals A microRNA detection system based on padlock probes and rolling circle amplification

RNA ◽  
2006 ◽  
Vol 12 (9) ◽  
pp. 1747-1752 ◽  
Author(s):  
S. P. Jonstrup
Keyword(s):  
Detection System ◽  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
Padlock Probes ◽  
Microrna Detection

scholarly journals Padlock Probe Assay for Detection and Subtyping of Seasonal Influenza

2018 ◽  
Vol 64 (12) ◽  
pp. 1704-1712 ◽  
Author(s):  
Felix Neumann ◽  
Iván Hernández-Neuta ◽  
Malin Grabbe ◽  
Narayanan Madaboosi ◽  
Jan Albert ◽  
...  
Keyword(s):  
Seasonal Influenza ◽  
Rolling Circle Amplification ◽  
High Specificity ◽  
Clinical Samples ◽  
Padlock Probe ◽  
Rolling Circle ◽  
Diagnostic Assays ◽  
Padlock Probes ◽  
Probe Assay ◽  
Digital Quantification

Abstract BACKGROUND Influenza remains a constant threat worldwide, and WHO estimates that it affects 5% to 15% of the global population each season, with an associated 3 to 5 million severe cases and up to 500000 deaths. To limit the morbidity and the economic burden of influenza, improved diagnostic assays are needed. METHODS We developed a multiplexed assay for the detection and subtyping of seasonal influenza based on padlock probes and rolling circle amplification. The assay simultaneously targets all 8 genome segments of the 4 circulating influenza variants—A(H1N1), A(H3N2), B/Yamagata, and B/Victoria—and was combined with a prototype cartridge for inexpensive digital quantification. Characterized virus isolates and patient nasopharyngeal swabs were used for assay design and analytical validation. The diagnostic performance was assessed by blinded testing of 50 clinical samples analyzed in parallel with a commercial influenza assay, Simplexa™ Flu A/B & RSV Direct. RESULTS The assay had a detection limit of 18 viral RNA copies and achieved 100% analytical and clinical specificity for differential detection and subtyping of seasonal circulating influenza variants. The diagnostic sensitivity on the 50 clinical samples was 77.5% for detecting influenza and up to 73% for subtyping seasonal variants. CONCLUSIONS We have presented a proof-of-concept padlock probe assay combined with an inexpensive digital readout for the detection and subtyping of seasonal influenza strains A and B. The demonstrated high specificity and multiplexing capability, together with the digital quantification, established the assay as a promising diagnostic tool for seasonal influenza.

scholarly journals On-Particle Rolling Circle Amplification-Based Core–Satellite Magnetic Superstructures for MicroRNA Detection

2018 ◽  
Vol 10 (3) ◽  
pp. 2957-2964 ◽  
Author(s):  
Bo Tian ◽  
Zhen Qiu ◽  
Jing Ma ◽  
Marco Donolato ◽  
Mikkel Fougt Hansen ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
Microrna Detection ◽  
Particle Rolling

scholarly journals SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections

2020 ◽  
Author(s):  
Alexandros Sountoulidis ◽  
Andreas Liontos ◽  
Hong Phuong Nguyen ◽  
Alexandra B. Firsova ◽  
Athanasios Fysikopoulos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rolling Circle Amplification ◽  
Marker Gene ◽  
Cell Types ◽  
Experimental Conditions ◽  
Rolling Circle ◽  
Padlock Probes ◽  
Tissue Sections ◽  
Specificity And Sensitivity

AbstractChanges in cell identities and positions underlie tissue development and disease progression. Although, single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell-states, spatially resolved single-cell mapping presents a challenging task. We developed SCRINSHOT (Single Cell Resolution INSitu Hybridization On Tissues), a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA is followed by circularization with SplintR ligase and rolling circle amplification (RCA) of the hybridized padlock probes. Sequential detection of RCA-products using fluorophore-labeled oligonucleotides profiles thousands of cells in tissue sections. We evaluated SCRINSHOT specificity and sensitivity on murine and human organs. SCRINSHOT quantification of marker gene expression shows high correlation with published scRNA-Seq data over a broad range of gene expression levels. We demonstrate the utility of SCRISHOT by mapping the locations of abundant and rare cell types along the murine airways. The amenability, multiplexity and quantitative qualities of SCRINSHOT facilitate single cell mRNA profiling of cell-state alterations in tissues under a variety of native and experimental conditions.

scholarly journals SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution

PLoS Biology ◽  
2020 ◽  
Vol 18 (11) ◽  
pp. e3000675
Author(s):  
Alexandros Sountoulidis ◽  
Andreas Liontos ◽  
Hong Phuong Nguyen ◽  
Alexandra B. Firsova ◽  
Athanasios Fysikopoulos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rolling Circle Amplification ◽  
Marker Gene ◽  
Cell Types ◽  
Experimental Conditions ◽  
Rolling Circle ◽  
Padlock Probes ◽  
Tissue Sections ◽  
Specificity And Sensitivity

Changes in cell identities and positions underlie tissue development and disease progression. Although single-cell mRNA sequencing (scRNA-Seq) methods rapidly generate extensive lists of cell states, spatially resolved single-cell mapping presents a challenging task. We developed SCRINSHOT (Single-Cell Resolution IN Situ Hybridization On Tissues), a sensitive, multiplex RNA mapping approach. Direct hybridization of padlock probes on mRNA is followed by circularization with SplintR ligase and rolling circle amplification (RCA) of the hybridized padlock probes. Sequential detection of RCA-products using fluorophore-labeled oligonucleotides profiles thousands of cells in tissue sections. We evaluated SCRINSHOT specificity and sensitivity on murine and human organs. SCRINSHOT quantification of marker gene expression shows high correlation with published scRNA-Seq data over a broad range of gene expression levels. We demonstrate the utility of SCRINSHOT by mapping the locations of abundant and rare cell types along the murine airways. The amenability, multiplexity, and quantitative qualities of SCRINSHOT facilitate single-cell mRNA profiling of cell-state alterations in tissues under a variety of native and experimental conditions.

scholarly journals Detection of Rotavirus Using Padlock Probes and Rolling Circle Amplification

PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e111874 ◽  
Author(s):  
Anja Mezger ◽  
Christina Öhrmalm ◽  
David Herthnek ◽  
Jonas Blomberg ◽  
Mats Nilsson
Keyword(s):  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
Padlock Probes

scholarly journals In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes

2004 ◽  
Vol 1 (3) ◽  
pp. 227-232 ◽  
Author(s):  
Chatarina Larsson ◽  
Jørn Koch ◽  
Anders Nygren ◽  
George Janssen ◽  
Anton K Raap ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Dna Molecules ◽  
Rolling Circle ◽  
Padlock Probes
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