Rolling Circle Amplification with Padlock Probes for In Situ Detection of RNA Analytes

2016 ◽  
pp. 99-105
Author(s):  
Anja Mezger ◽  
Malte Kühnemund ◽  
Mats Nilsson
Keyword(s):  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
Padlock Probes ◽  
In Situ Detection

In Situ Detection of Messenger RNA Using Digoxigenin-Labeled Oligonucleotides and Rolling Circle Amplification

2001 ◽  
Vol 70 (3) ◽  
pp. 281-288 ◽  
Author(s):  
Yi Zhou ◽  
Margaret Calciano ◽  
Stefan Hamann ◽  
J.H. Leamon ◽  
Tod Strugnell ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
In Situ Detection

scholarly journals In situ Detection of Specific DNA Double Strand Breaks using Rolling Circle Amplification

Cell Cycle ◽  
2005 ◽  
Vol 4 (12) ◽  
pp. 1767-1773 ◽  
Author(s):  
Jia Li ◽  
C.S.H. Young ◽  
Paul M. Lizardia ◽  
David F. Stern
Keyword(s):  
Rolling Circle Amplification ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Rolling Circle ◽  
Strand Breaks ◽  
In Situ Detection

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

scholarly journals Development of an in situ assay for simultaneous detection of the genomic and replicative form of PCV2 using padlock probes and rolling circle amplification

2011 ◽  
Vol 8 (1) ◽  
pp. 37 ◽  
Author(s):  
Sara Henriksson ◽  
Anne-Lie Blomström ◽  
Lisbeth Fuxler ◽  
Caroline Fossum ◽  
Mikael Berg ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Simultaneous Detection ◽  
Replicative Form ◽  
Rolling Circle ◽  
Padlock Probes ◽  
In Situ Assay

scholarly journals Detection of Low-Copy-Number Genomic DNA Sequences in Individual Bacterial Cells by Using Peptide Nucleic Acid-Assisted Rolling-Circle Amplification and Fluorescence In Situ Hybridization

2007 ◽  
Vol 73 (7) ◽  
pp. 2324-2328 ◽  
Author(s):  
Irina Smolina ◽  
Charles Lee ◽  
Maxim Frank-Kamenetskii
Keyword(s):  
Dna Sequences ◽  
Peptide Nucleic Acid ◽  
Rolling Circle Amplification ◽  
Bacterial Genome ◽  
Bacterial Cells ◽  
Rolling Circle ◽  
Low Copy Number ◽  
Short Signature ◽  
In Situ Detection

ABSTRACT An approach is proposed for in situ detection of short signature DNA sequences present in single copies per bacterial genome. The site is locally opened by peptide nucleic acids, and a circular oligonucleotide is assembled. The amplicon generated by rolling circle amplification is detected by hybridization with fluorescently labeled decorator probes.

scholarly journals Direct RNA targeted transcriptomic profiling in tissue using Hybridization-based RNA In Situ Sequencing (HybRISS)

2020 ◽  
Author(s):  
Hower Lee ◽  
Sergio Marco Salas ◽  
Daniel Gyllborg ◽  
Mats Nilsson
Keyword(s):  
De Novo ◽  
Detection Efficiency ◽  
Rolling Circle Amplification ◽  
Fold Increase ◽  
Data Interpretation ◽  
Rolling Circle ◽  
Padlock Probes ◽  
Multiple Transcripts ◽  
Detection Approach

Highly multiplexed spatial mapping of multiple transcripts within tissues allows for investigation of the transcriptomic and cellular diversity of mammalian organs previously unseen. Here we explore the possibilities of a direct RNA (dRNA) detection approach incorporating the use of padlock probes and rolling circle amplification in combination with hybridization-based in situ sequencing (HybISS) chemistry. We benchmark a dRNA targeting kit that circumvents the standard reverse transcription limiting, cDNA-based in situ sequencing (ISS). We found a five-fold increase in transcript detection efficiency when compared to cDNA-based ISS and also validated its multiplexing capability by targeting a curated panel of 50 genes from previous publications on mouse brain sections, leading to additional data interpretation such as de novo cell typing. With this increased efficiency, we maintain specificity, multiplexing capabilities and ease of implementation. Overall, the dRNA chemistry shows significant improvements in target detection efficiency, closing the gap between the gold standard of fluorescent in situ hybridization (FISH) based technologies and opens up possibilities to explore new biological questions previously not possible with cDNA-based ISS, nor with FISH.

Rolling Circle Amplification of Cyclizable Dna Probes by ∅29 Dna Polymerase: A Tool for in Situ Single-Copy Gene Detection.

1997 ◽  
Vol 3 (S2) ◽  
pp. 201-202
Author(s):  
Paul M. Lizardi ◽  
Patricia Bray-Ward ◽  
David C. Ward
Keyword(s):  
Dna Polymerase ◽  
Rolling Circle Amplification ◽  
Single Copy ◽  
Rolling Circle Replication ◽  
Gene Detection ◽  
Rolling Circle ◽  
Padlock Probes ◽  
Cytological Localization ◽  
High Degree

Oligonucleotide probes that can be cyclized by ligation (“padlock probes”) provide a very high degree of recognition specificity. Nilsson et al. have demonstrated the used of padlock probes for the cytological localization of alphoid repeats in chromosome 12. We have been extending the use of padlock probes to the detection of single copy sequences, and with this in mind have explored the amplification of DNA circles.We designed a primer complementary to the arbitrary backbone (non-probing) sequence of a 92-base closed circular probe oligonucleotide and investigated the kinetics of rolling circle replication. Using the highly processive, strand-displacing DNA polymerase of phage ∅29 (kindly provided by Dr. Margarita Salas, CSIC, Madrid, Spain) we demonstrated that several hundred tandem copies of the circular oligonucleotide are generated in a few minutes of incubation at 32°C. Because the amplified DNA remains hybridized to the circle in a rolling circle reaction, this method of amplification offers unique advantages for in situ gene detection since the amplified DNA can not diffuse away from the site of synthesis.

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