A Dumbbell Probe-mediated Rolling Circle Amplification Strategy for Highly Sensitive MicroRNA Detection

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 Jun 16

PMID 20547593

Citations 27

Authors

Yuntao Zhou

Qing Huang

Jimin Gao

Jianxin Lu

Xizhong Shen

Chunhai Fan

Affiliations

Soon will be listed here.

Abstract

We herein report the design of a dumbbell-shaped DNA probe that integrates target-binding, amplification and signaling within one multifunctional design. The dumbbell probe can initiate rolling circle amplification (D-RCA) in the presence of specific microRNA (miRNA) targets. This D-RCA-based miRNA strategy allows quantification of miRNA with very low quantity of RNA samples. The femtomolar sensitivity of D-RCA compares favorably with other existing technologies. More significantly, the dynamic range of D-RCA is extremely large, covering eight orders of magnitude. We also demonstrate miRNA quantification with this highly sensitive and inexpensive D-RCA strategy in clinical samples.

Citing Articles

A label-free aptasensing method for detecting SARS-CoV-2 virus antigen by using dumbbell probe-mediated circle-to-circle amplification.

Wang Z, He S, Zhang C, Xu D Anal Bioanal Chem. 2024; 416(8):1961-1970.

PMID: 38349532 DOI: 10.1007/s00216-024-05195-y.

Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis.

Zhao M, Wang R, Yang K, Jiang Y, Peng Y, Li Y Acta Pharm Sin B. 2023; 13(3):916-941.

PMID: 36970219 PMC: 10031267. DOI: 10.1016/j.apsb.2022.10.019.

Novel Detection Method for Circulating EGFR Tumor DNA Using Gravitationally Condensed Gold Nanoparticles and Catalytic Walker DNA.

You J, Park C, Jang K, Park J, Na S Materials (Basel). 2022; 15(9).

PMID: 35591635 PMC: 9101948. DOI: 10.3390/ma15093301.

A Homogeneous Label-Free Electrochemical microRNA Biosensor Coupling With G-Triplex/Methylene Blue Complex and λ-Exonuclease-Assisted Recycling Amplification.

Meng Y, Chen F, Jiang M, Guo Q, Wang Y, Wang J Front Chem. 2021; 9:753253.

PMID: 34805092 PMC: 8600312. DOI: 10.3389/fchem.2021.753253.

Emerging Role of isomiRs in Cancer: State of the Art and Recent Advances.

Zelli V, Compagnoni C, Capelli R, Corrente A, Cornice J, Vecchiotti D Genes (Basel). 2021; 12(9).

PMID: 34573429 PMC: 8469436. DOI: 10.3390/genes12091447.

References

Calin G, Liu C, Sevignani C, Ferracin M, Felli N, Dumitru C . MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci U S A. 2004; 101(32):11755-60. PMC: 511048. DOI: 10.1073/pnas.0404432101. View

Ambros V . microRNAs: tiny regulators with great potential. Cell. 2002; 107(7):823-6. DOI: 10.1016/s0092-8674(01)00616-x. View

Valoczi A, Hornyik C, Varga N, Burgyan J, Kauppinen S, Havelda Z . Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res. 2004; 32(22):e175. PMC: 545470. DOI: 10.1093/nar/gnh171. View

Murakami Y, Yasuda T, Saigo K, Urashima T, Toyoda H, Okanoue T . Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene. 2005; 25(17):2537-45. DOI: 10.1038/sj.onc.1209283. View

Thomson J, Parker J, Perou C, Hammond S . A custom microarray platform for analysis of microRNA gene expression. Nat Methods. 2005; 1(1):47-53. DOI: 10.1038/nmeth704. View

Mestdagh P, Feys T, Bernard N, Guenther S, Chen C, Speleman F . High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA. Nucleic Acids Res. 2008; 36(21):e143. PMC: 2588502. DOI: 10.1093/nar/gkn725. View

Blenkiron C, Goldstein L, Thorne N, Spiteri I, Chin S, Dunning M . MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol. 2007; 8(10):R214. PMC: 2246288. DOI: 10.1186/gb-2007-8-10-r214. View

Bartel D . MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116(2):281-97. DOI: 10.1016/s0092-8674(04)00045-5. View

Jiang J, Lee E, Gusev Y, Schmittgen T . Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res. 2005; 33(17):5394-403. PMC: 1236977. DOI: 10.1093/nar/gki863. View

10.

Bonnet G, Tyagi S, Libchaber A, Kramer F . Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc Natl Acad Sci U S A. 1999; 96(11):6171-6. PMC: 26854. DOI: 10.1073/pnas.96.11.6171. View

11.

Harfe B . MicroRNAs in vertebrate development. Curr Opin Genet Dev. 2005; 15(4):410-5. DOI: 10.1016/j.gde.2005.06.012. View

12.

Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik A, Hentze M . A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA. 2006; 12(5):913-20. PMC: 1440900. DOI: 10.1261/rna.2332406. View

13.

Zipper H, Brunner H, Bernhagen J, Vitzthum F . Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res. 2004; 32(12):e103. PMC: 484200. DOI: 10.1093/nar/gnh101. View

14.

Liu G, Wan Y, Gau V, Zhang J, Wang L, Song S . An enzyme-based E-DNA sensor for sequence-specific detection of femtomolar DNA targets. J Am Chem Soc. 2008; 130(21):6820-5. DOI: 10.1021/ja800554t. View

15.

Chen J, Lozach J, Garcia E, Barnes B, Luo S, Mikoulitch I . Highly sensitive and specific microRNA expression profiling using BeadArray technology. Nucleic Acids Res. 2008; 36(14):e87. PMC: 2504321. DOI: 10.1093/nar/gkn387. View

16.

Berezikov E, van Tetering G, Verheul M, van de Belt J, Van Laake L, Vos J . Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res. 2006; 16(10):1289-98. PMC: 1581438. DOI: 10.1101/gr.5159906. View

17.

Murakami T, Sumaoka J, Komiyama M . Sensitive isothermal detection of nucleic-acid sequence by primer generation-rolling circle amplification. Nucleic Acids Res. 2008; 37(3):e19. PMC: 2647323. DOI: 10.1093/nar/gkn1014. View

18.

Dahl F, Baner J, Gullberg M, Mendel-Hartvig M, Landegren U, Nilsson M . Circle-to-circle amplification for precise and sensitive DNA analysis. Proc Natl Acad Sci U S A. 2004; 101(13):4548-53. PMC: 384784. DOI: 10.1073/pnas.0400834101. View

19.

Li J, Chu Y, Lee B, Xie X . Enzymatic signal amplification of molecular beacons for sensitive DNA detection. Nucleic Acids Res. 2008; 36(6):e36. PMC: 2346604. DOI: 10.1093/nar/gkn033. View

20.

Chen C, Ridzon D, Broomer A, Zhou Z, Lee D, Nguyen J . Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005; 33(20):e179. PMC: 1292995. DOI: 10.1093/nar/gni178. View