Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 30 September 1994:
Vol. 265. no. 5181, pp. 2085 - 2088
DOI: 10.1126/science.7522346
Prev | Table of Contents | Next

Articles

Science, Vol 265, Issue 5181, 2085-2088
Copyright © 1994 by American Association for the Advancement of Science

articles

Padlock probes: circularizing oligonucleotides for localized DNA detection

M Nilsson, H Malmgren, M Samiotaki, M Kwiatkowski, BP Chowdhary, and U Landegren

Beijer Laboratory, Department of Medical Genetics, Biomedical Center, Uppsala, Sweden.

Nucleotide sequence information derived from DNA segments of the human and other genomes is accumulating rapidly. However, it frequently proves difficult to use such short DNA segments to identify clones in genomic libraries or fragments in blots of the whole genome or for in situ analysis of chromosomes. Oligonucleotide probes, consisting of two target-complementary segments, connected by a linker sequence, were designed. Upon recognition of the specific nucleic acid molecule the ends of the probes were joined through the action of a ligase, creating circular DNA molecules catenated to the target sequence. These probes thus provide highly specific detection with minimal background.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Glycosylases and AP-cleaving enzymes as a general tool for probe-directed cleavage of ssDNA targets.
W. M. Howell, I. Grundberg, M. Faryna, U. Landegren, and M. Nilsson (2010)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Robust Detection and Identification of Multiple Oomycetes and Fungi in Environmental Samples by Using a Novel Cleavable Padlock Probe-Based Ligation Detection Assay.
R. van Doorn, M. Slawiak, M. Szemes, A. M. Dullemans, P. Bonants, G. A. Kowalchuk, and C. D. Schoen (2009)
Appl. Envir. Microbiol. 75, 4185-4193
   Abstract »    Full Text »    PDF »
Finding the fifth base: Genome-wide sequencing of cytosine methylation.
R. Lister and J. R. Ecker (2009)
Genome Res. 19, 959-966
   Abstract »    Full Text »    PDF »
Multiplexed Genotyping of Methicillin-Resistant Staphylococcus aureus Isolates by Use of Padlock Probes and Tag Microarrays.
K. Kurt, A. Alderborn, M. Nilsson, B. Strommenger, W. Witte, and U. Nubel (2009)
J. Clin. Microbiol. 47, 577-585
   Abstract »    Full Text »    PDF »
Sensitive isothermal detection of nucleic-acid sequence by primer generation-rolling circle amplification.
T. Murakami, J. Sumaoka, and M. Komiyama (2009)
Nucleic Acids Res. 37, e19
   Abstract »    Full Text »    PDF »
A single molecule array for digital targeted molecular analyses.
J. Goransson, C. Wahlby, M. Isaksson, W. M. Howell, J. Jarvius, and M. Nilsson (2009)
Nucleic Acids Res. 37, e7
   Abstract »    Full Text »    PDF »
Hairpin ribozyme-antisense RNA constructs can act as molecular lassos.
A. Dallas, S. V. Balatskaya, T.-C. Kuo, H. Ilves, A. V. Vlassov, R. L. Kaspar, K. O. Kisich, S. A. Kazakov, and B. H. Johnston (2008)
Nucleic Acids Res. 36, 6752-6766
   Abstract »    Full Text »    PDF »
Keeping Up With the Next Generation: Massively Parallel Sequencing in Clinical Diagnostics.
J. R. ten Bosch and W. W. Grody (2008)
J. Mol. Diagn. 10, 484-492
   Abstract »    Full Text »    PDF »
A comprehensive assay for targeted multiplex amplification of human DNA sequences.
S. Krishnakumar, J. Zheng, J. Wilhelmy, M. Faham, M. Mindrinos, and R. Davis (2008)
PNAS 105, 9296-9301
   Abstract »    Full Text »    PDF »
In Situ Detection of Anaplasma spp. by DNA Target-Primed Rolling-Circle Amplification of a Padlock Probe and Intracellular Colocalization with Immunofluorescently Labeled Host Cell von Willebrand Factor.
H. L. Wamsley and A. F. Barbet (2008)
J. Clin. Microbiol. 46, 2314-2319
   Abstract »    Full Text »    PDF »
Simultaneous Genotyping of All Hemagglutinin and Neuraminidase Subtypes of Avian Influenza Viruses by Use of Padlock Probes.
P. Gyarmati, T. Conze, S. Zohari, N. LeBlanc, M. Nilsson, U. Landegren, J. Baner, and S. Belak (2008)
J. Clin. Microbiol. 46, 1747-1751
   Abstract »    Full Text »    PDF »
Enzymatic signal amplification of molecular beacons for sensitive DNA detection.
J. J. Li, Y. Chu, B. Y.-H. Lee, and X. S. Xie (2008)
Nucleic Acids Res. 36, e36
   Abstract »    Full Text »    PDF »
Anti-gene padlocks eliminate Escherichia coli based on their genotype.
C. Shi, A. R. Parker, L. Hua, C. N. Morrell, S. C. Lee, V. Bandaru, J. S. Dumler, T. C. Wu, and J. R. Eshleman (2008)
J. Antimicrob. Chemother. 61, 262-272
   Abstract »    Full Text »    PDF »
Determination of the Ex Vivo Rates of Human Immunodeficiency Virus Type 1 Reverse Transcription by Using Novel Strand-Specific Amplification Analysis.
D. C. Thomas, Y. A. Voronin, G. N. Nikolenko, J. Chen, W.-S. Hu, and V. K. Pathak (2007)
J. Virol. 81, 4798-4807
   Abstract »    Full Text »    PDF »
A microRNA detection system based on padlock probes and rolling circle amplification.
S. P. Jonstrup, J. Koch, and J. Kjems (2006)
RNA 12, 1747-1752
   Abstract »    Full Text »    PDF »
Molecular Zipper: a fluorescent probe for real-time isothermal DNA amplification.
J. Yi, W. Zhang, and D. Y. Zhang (2006)
Nucleic Acids Res. 34, e81
   Abstract »    Full Text »    PDF »
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix.
P. Yakovchuk, E. Protozanova, and M. D. Frank-Kamenetskii (2006)
Nucleic Acids Res. 34, 564-574
   Abstract »    Full Text »    PDF »
Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA..
E. Pettersson, M. Lindskog, J. Lundeberg, and A. Ahmadian (2006)
Nucleic Acids Res. 34, e49
   Abstract »    Full Text »    PDF »
Diagnostic application of padlock probes--multiplex detection of plant pathogens using universal microarrays.
M. Szemes, P. Bonants, M. de Weerdt, J. Baner, U. Landegren, and C. D. Schoen (2005)
Nucleic Acids Res. 33, e70
   Abstract »    Full Text »    PDF »
Analysis of T-Cell Receptor V{beta} Gene Repertoires after Immune Stimulation and in Malignancy by Use of Padlock Probes and Microarrays.
J. Baner, P. Marits, M. Nilsson, O. Winqvist, and U. Landegren (2005)
Clin. Chem. 51, 768-775
   Abstract »    Full Text »    PDF »
Competitive enzymatic reaction to control allele-specific extensions.
E. Hultin, M. Kaller, A. Ahmadian, and J. Lundeberg (2005)
Nucleic Acids Res. 33, e48
   Abstract »    Full Text »    PDF »
Marking of specific sequences in double-stranded DNA molecules--SNP detection and direct observation.
Y. Shigemori, H. Haruta, T. Okada, and M. Oishi (2004)
Genome Res. 14, 2478-2485
   Abstract »    Full Text »    PDF »
Principles of pharmacogenetics--implications for the anaesthetist.
G. Iohom, D. Fitzgerald, and A. J. Cunningham (2004)
Br. J. Anaesth. 93, 440-450
   Full Text »    PDF »
Circle-to-circle amplification for precise and sensitive DNA analysis.
F. Dahl, J. Baner, M. Gullberg, M. Mendel-Hartvig, U. Landegren, and M. Nilsson (2004)
PNAS 101, 4548-4553
   Abstract »    Full Text »    PDF »
SNPWaveTM: a flexible multiplexed SNP genotyping technology.
M. J. T. van Eijk, J. L. N. Broekhof, H. J. A. van der Poel, R. C. J. Hogers, H. Schneiders, J. Kamerbeek, E. Verstege, J. W. van Aart, H. Geerlings, J. B. Buntjer, et al. (2004)
Nucleic Acids Res. 32, e47
   Abstract »    Full Text »    PDF »
Ligase-mediated construction of branched DNA strands: a novel DNA joining activity catalyzed by T4 DNA ligase.
M. Mendel-Hartvig, A. Kumar, and U. Landegren (2004)
Nucleic Acids Res. 32, e2
   Abstract »    Full Text »    PDF »
Parallel gene analysis with allele-specific padlock probes and tag microarrays.
J. Baner, A. Isaksson, E. Waldenstrom, J. Jarvius, U. Landegren, and M. Nilsson (2003)
Nucleic Acids Res. 31, e103
   Abstract »    Full Text »    PDF »
SNP Genotyping and Molecular Haplotyping of DNA Pools.
P.-Y. KWOK and M. XIAO (2003)
Cold Spring Harb Symp Quant Biol 68, 65-68
   Abstract »    PDF »
Single nucleotide polymorphism seeking long term association with complex disease.
B. W. Kirk, M. Feinsod, R. Favis, R. M. Kliman, and F. Barany (2002)
Nucleic Acids Res. 30, 3295-3311
   Abstract »    Full Text »    PDF »
Real-time monitoring of rolling-circle amplification using a modified molecular beacon design.
M. Nilsson, M. Gullberg, F. Dahl, K. Szuhai, and A. K. Raap (2002)
Nucleic Acids Res. 30, e66
   Abstract »    Full Text »    PDF »
Integration of DNA ligation and rolling circle amplification for the homogeneous, end-point detection of single nucleotide polymorphisms.
J. Pickering, A. Bamford, V. Godbole, J. Briggs, G. Scozzafava, P. Roe, C. Wheeler, F. Ghouze, and S. Cuss (2002)
Nucleic Acids Res. 30, e60
   Abstract »    Full Text »    PDF »
Multiplex Pyrosequencing.
N. Pourmand, E. Elahi, R. W. Davis, and M. Ronaghi (2002)
Nucleic Acids Res. 30, e31
   Abstract »    Full Text »    PDF »
Rolling-circle amplification under topological constraints.
H. Kuhn, V. V. Demidov, and M. D. Frank-Kamenetskii (2002)
Nucleic Acids Res. 30, 574-580
   Abstract »    Full Text »    PDF »
L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs).
X. Qi, S. Bakht, K. M. Devos, M. D. Gale, and A. Osbourn (2001)
Nucleic Acids Res. 29, e116
   Abstract »    Full Text »    PDF »
RNA-templated DNA ligation for transcript analysis.
M. Nilsson, D.-O. Antson, G. Barbany, and U. Landegren (2001)
Nucleic Acids Res. 29, 578-581
   Abstract »    Full Text »    PDF »
Alpha Satellite DNA Variant-Specific Oligoprobes Differing by a Single Base Can Distinguish Chromosome 15 Homologs.
C. L. O'Keefe and A. G. Matera (2000)
Genome Res. 10, 1342-1350
   Abstract »    Full Text »
PCR-generated padlock probes detect single nucleotide variation in genomic DNA.
D.-O. Antson, A. Isaksson, U. Landegren, and M. Nilsson (2000)
Nucleic Acids Res. 28, e58
   Abstract »    Full Text »    PDF »
Optimised ligation of oligonucleotides by thermal ligases: comparison of Thermus scotoductus and Rhodothermus marinus DNA ligases to other thermophilic ligases.
J. N. Housby, S. H. Thorbjarnardottir, Z. O. Jonsson, and E. M. Southern (2000)
Nucleic Acids Res. 28, e10
   Abstract »    Full Text »    PDF »
Padlock oligonucleotides for duplex DNA based on sequence-specific triple helix formation.
C. Escude, T. Garestier, and C. Helene (1999)
PNAS 96, 10603-10607
   Abstract »    Full Text »    PDF »
Sensitive mRNA Detection by Fluorescence In Situ Hybridization Using Horseradish Peroxidase-labeled Oligodeoxynucleotides and Tyramide Signal Amplification.
M. P.C. van de Corput, R. W. Dirks, R. P.M. van Gijlswijk, E. van Binnendijk, C. M. Hattinger, R. A. de Paus, J. E. Landegent, and A. K. Raap (1998)
J. Histochem. Cytochem. 46, 1249-1260
   Abstract »    Full Text »
Reading Bits of Genetic Information: Methods for Single-Nucleotide Polymorphism Analysis.
U. Landegren, M. Nilsson, and P.-Y. Kwok (1998)
Genome Res. 8, 769-776
   Full Text »
Detection of DNA point mutations and mRNA expression levels by rolling circle amplification in individual cells.
A. T. Christian, M. S. Pattee, C. M. Attix, B. E. Reed, K. J. Sorensen, and J. D. Tucker (2001)
PNAS 98, 14238-14243
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)