Making ends meet in genetic analysis using padlock probes

Nilsson, Mats; Banér, Johan; Mendel-Hartvig, Maritha; Dahl, Fredrik A.; Antson, Dan-Oscar; Gullberg, Mats; Landegren, Ulf

doi:10.1002/humu.10073

Cited by 43 publications

(19 citation statements)

References 21 publications

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“…The miRNA that is used as a template can subsequently be used as primer for rolling circle amplification, thereby linearly amplifying the target sequence in a process that has been shown to be highly quantitative ( Fig. 1; Nilsson et al 2002). In this study we demonstrate that the padlock probe technology provides a simple low-tech method for analysis of miRNAs quantitatively in a few nanograms of total RNA.…”

Section: Introductionmentioning

confidence: 68%

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

Jonstrup¹,

Koch²,

Kjems³

2006

RNA

209

143

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The differential expression and the regulatory roles of microRNAs (miRNAs) are being studied intensively these years. Their minute size of only 19-24 nucleotides and strong sequence similarity among related species call for enhanced methods for reliable detection and quantification. Moreover, miRNA expression is generally restricted to a limited number of specific cells within an organism and therefore requires highly sensitive detection methods. Here we present a simple and reliable miRNA detection protocol based on padlock probes and rolling circle amplification. It can be performed without specialized equipment and is capable of measuring the content of specific miRNAs in a few nanograms of total RNA.

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Section: Introductionmentioning

confidence: 68%

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

Jonstrup¹,

Koch²,

Kjems³

2006

RNA

209

143

View full text Add to dashboard Cite

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“…The PLP methodology was chosen because of its high multiplexing capacity, which constrains more conventional PCR methods (10,15). PLPs also reduce the number of conserved regions needed on target nucleic acids because both probe arms bind to a single region (2,3).…”

Section: Discussionmentioning

confidence: 99%

Simultaneous Genotyping of All Hemagglutinin and Neuraminidase Subtypes of Avian Influenza Viruses by Use of Padlock Probes

et al. 2008

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A subtyping assay for both the hemagglutinin (HA) and neuraminidase (NA) surface antigens of the avian influenza virus (AIV) has been developed. The method uses padlock probe chemistry combined with a microarray output for detection. The outstanding feature of this assay is its capability to designate both the HA and the NA of an AIV sample from a single reaction mixture. A panel of 77 influenza virus strains was tested representing the entire assortment of the two antigens. One hundred percent (77/77) of the samples tested were identified as AIV, and 97% (75/77) were subtyped correctly in accordance with previous examinations performed by classical diagnostic methods. Testing of heterologous pathogens verified the specificity of the assay. This assay is a convenient and practical tool for the study of AIVs, providing important HA and NA data more rapidly than conventional methods.

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“…18,24 However, the number of colors that can be used in an in situ experiment is limited by the number of haptens available, and that can be incorporated in the probes. We have, however, successfully been able to directly label the probes by incorporating fluorescence-labeled nucleotides during PCR, which increases the multiplexing possibilities substantially (unpublished results).…”

Section: Discussionmentioning

confidence: 99%

PCR-generated padlock probes distinguish homologous chromosomes through quantitative fluorescence analysis

Antson

Mendel-Hartvig²,

Landegren³

et al. 2003

Eur J Hum Genet

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Conventional cytogenetic techniques can distinguish homologous chromosomes in a qualitative manner based upon obvious morphological features or using in situ hybridization methods that yield qualitative data. We have developed a method for quantitative genotyping of single-nucleotide variants in situ using circularizable DNA probes, so-called padlock probes, targeting two different alpha satellite repeat variants present in human chromosome 7 centromeres, and a single-nucleotide variation in alpha satellite repeats on human chromosome 15 centromeres. By using these PCR-generated padlock probes, we could quantitatively distinguish homologous chromosomes and follow the transmission of the chromosomes by in situ analysis during three consecutive generations.

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Making ends meet in genetic analysis using padlock probes

Cited by 43 publications

References 21 publications

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

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

Simultaneous Genotyping of All Hemagglutinin and Neuraminidase Subtypes of Avian Influenza Viruses by Use of Padlock Probes

PCR-generated padlock probes distinguish homologous chromosomes through quantitative fluorescence analysis

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