Target-driven DNA Association to Initiate Cyclic Assembly of Hairpins for Biosensing and Logic Gate Operation

Overview

Journal Chem Sci

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2017 Dec 9

PMID 29218202

Citations 11

Authors

Yuehua Guo

Jie Wu

Huangxian Ju

Affiliations

Soon will be listed here.

Abstract

A target-driven DNA association was designed to initiate cyclic assembly of hairpins, which led to an enzyme-free amplification strategy for detection of a nucleic acid or aptamer substrate and flexible construction of logic gates. The cyclic system contained two ssDNA (S1 and S2) and two hairpins (H1 and H2). These ssDNA could co-recognize the target to produce an S1-target-S2 structure, which brought their toehold and branch-migration domains into close proximity to initiate the cyclic assembly of hairpins. The assembly product further induced the dissociation of a double-stranded probe DNA (Q:F) toehold-mediated strand displacement to switch the fluorescence signal. This method could detect DNA and ATP as model analytes down to 21.6 pM and 38 nM, respectively. By designing different DNA input strands, the "AND", "INHIBIT" and "NAND" logic gates could be activated to achieve the output signal. The proposed biosensing and logic gate operation platform showed potential applications in disease diagnosis.

Citing Articles

Signal amplified colorimetric nucleic acid detection based on autocatalytic hairpin assembly.

Liu Y, Jin L, Mao J, Deng R, Lin F, Cheng Y RSC Adv. 2024; 14(24):17152-17157.

PMID: 38808241 PMC: 11130644. DOI: 10.1039/d4ra01982b.

DNA Aptamer Beacon Probe (ABP) for Monitoring of Adenosine Triphosphate Level in SW480 Cancer Cells Treated with Glycolysis Inhibitor 2-Deoxyglucose.

Ratajczak K, Stobiecka M Int J Mol Sci. 2023; 24(11).

PMID: 37298245 PMC: 10253522. DOI: 10.3390/ijms24119295.

Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications.

Fan D, Wang J, Wang E, Dong S Adv Sci (Weinh). 2020; 7(24):2001766.

PMID: 33344121 PMC: 7740092. DOI: 10.1002/advs.202001766.

Logic Gates Based on DNA Aptamers.

Andrianova M, Kuznetsov A Pharmaceuticals (Basel). 2020; 13(11).

PMID: 33238657 PMC: 7700249. DOI: 10.3390/ph13110417.

Integrating CRISPR-Cas12a with a DNA circuit as a generic sensing platform for amplified detection of microRNA.

Peng S, Tan Z, Chen S, Lei C, Nie Z Chem Sci. 2020; 11(28):7362-7368.

PMID: 33133487 PMC: 7553042. DOI: 10.1039/d0sc03084h.

References

Beissenhirtz M, Elnathan R, Weizmann Y, Willner I . The aggregation of Au nanoparticles by an autonomous DNA machine detects viruses. Small. 2007; 3(3):375-9. DOI: 10.1002/smll.200600450. View

Zhang D, Turberfield A, Yurke B, Winfree E . Engineering entropy-driven reactions and networks catalyzed by DNA. Science. 2007; 318(5853):1121-5. DOI: 10.1126/science.1148532. View

Yin P, Choi H, Calvert C, Pierce N . Programming biomolecular self-assembly pathways. Nature. 2008; 451(7176):318-22. DOI: 10.1038/nature06451. View

Jin K, Shin S, Ahn B, Rho Y, Kim S, Ree M . pH-dependent structures of an i-motif DNA in solution. J Phys Chem B. 2009; 113(7):1852-6. DOI: 10.1021/jp808186z. View

Zuo X, Xiao Y, Plaxco K . High specificity, electrochemical sandwich assays based on single aptamer sequences and suitable for the direct detection of small-molecule targets in blood and other complex matrices. J Am Chem Soc. 2009; 131(20):6944-5. PMC: 2994717. DOI: 10.1021/ja901315w. View

Niu S, Jiang Y, Zhang S . Fluorescence detection for DNA using hybridization chain reaction with enzyme-amplification. Chem Commun (Camb). 2010; 46(18):3089-91. DOI: 10.1039/c000166j. View

Elbaz J, Lioubashevski O, Wang F, Remacle F, Levine R, Willner I . DNA computing circuits using libraries of DNAzyme subunits. Nat Nanotechnol. 2010; 5(6):417-22. DOI: 10.1038/nnano.2010.88. View

Huang J, Wu Y, Chen Y, Zhu Z, Yang X, Yang C . Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids. Angew Chem Int Ed Engl. 2010; 50(2):401-4. DOI: 10.1002/anie.201005375. View

Wang Z, Elbaz J, Willner I . DNA machines: bipedal walker and stepper. Nano Lett. 2010; 11(1):304-9. DOI: 10.1021/nl104088s. View

10.

Zhang D, Seelig G . Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem. 2011; 3(2):103-13. DOI: 10.1038/nchem.957. View

11.

Muscat R, Bath J, Turberfield A . A programmable molecular robot. Nano Lett. 2011; 11(3):982-7. DOI: 10.1021/nl1037165. View

12.

Zhao C, Wu L, Ren J, Qu X . A label-free fluorescent turn-on enzymatic amplification assay for DNA detection using ligand-responsive G-quadruplex formation. Chem Commun (Camb). 2011; 47(19):5461-3. DOI: 10.1039/c1cc11396h. View

13.

Freeman R, Liu X, Willner I . Chemiluminescent and chemiluminescence resonance energy transfer (CRET) detection of DNA, metal ions, and aptamer-substrate complexes using hemin/G-quadruplexes and CdSe/ZnS quantum dots. J Am Chem Soc. 2011; 133(30):11597-604. DOI: 10.1021/ja202639m. View

14.

Li B, Ellington A, Chen X . Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res. 2011; 39(16):e110. PMC: 3167626. DOI: 10.1093/nar/gkr504. View

15.

Liu X, Freeman R, Golub E, Willner I . Chemiluminescence and chemiluminescence resonance energy transfer (CRET) aptamer sensors using catalytic hemin/G-quadruplexes. ACS Nano. 2011; 5(9):7648-55. DOI: 10.1021/nn202799d. View

16.

Wang F, Elbaz J, Orbach R, Magen N, Willner I . Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires. J Am Chem Soc. 2011; 133(43):17149-51. DOI: 10.1021/ja2076789. View

17.

Chen X . Expanding the rule set of DNA circuitry with associative toehold activation. J Am Chem Soc. 2011; 134(1):263-71. PMC: 3260326. DOI: 10.1021/ja206690a. View

18.

Shimron S, Wang F, Orbach R, Willner I . Amplified detection of DNA through the enzyme-free autonomous assembly of hemin/G-quadruplex DNAzyme nanowires. Anal Chem. 2012; 84(2):1042-8. DOI: 10.1021/ac202643y. View

19.

McKee M, Milnes P, Bath J, Stulz E, OReilly R, Turberfield A . Programmable one-pot multistep organic synthesis using DNA junctions. J Am Chem Soc. 2012; 134(3):1446-9. DOI: 10.1021/ja2101196. View

20.

Zheng A, Li J, Wang J, Song X, Chen G, Yang H . Enzyme-free signal amplification in the DNAzyme sensor via target-catalyzed hairpin assembly. Chem Commun (Camb). 2012; 48(25):3112-4. DOI: 10.1039/c2cc30305a. View