Binding-Induced Formation of DNA Three-Way Junctions and Its Application to Protein Detection and DNA Strand Displacement

Li, Feng; Lin, Yanwen; Le, X. Chris

doi:10.1021/ac402179a

Cited by 86 publications

(47 citation statements)

References 28 publications

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“…Inspired by this strategy, in this paper, we have developed a robust GO nanoprobe analysis platform based on proximity binding assay [28][29][30][31][32][33][34] integrated with Pb 2+ -DNAzyme assistant probe recycling to achieve signal enhancement for detection of ATP activity and imaging of ATP in living cells (Scheme 1). The proximity binding of two aptamers to ATP leads to the release of the enzymatic sequences, which hybridize with the FAM-linked substrate strand on the graphene oxide (GO) surface to form the ion-dependent DNAzyme.…”

mentioning

confidence: 99%

Proximity hybridization triggered strand displacement and DNAzyme assisted strand recycling for ATP fluorescence detection in vitro and imaging in living cells

Gao

Yao

et al. 2018

RSC Adv.

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We developed a novel strategy for ATP detection in vitro and imaging in living cells based on integrating proximity hybridization-induced strand displacement and metal ion-dependent DNAzyme recycling amplification. Four DNA oligonucleotides were used in the sensing system including two aptamer probes, enzymatic sequences and FAM-linked substrate strands. Upon the addition of ATP, the proximity binding of two aptamers to ATP led to the release of the enzymatic sequences, which hybridized with the FAM-linked substrate strand on the graphene oxide (GO) surface to form the ion-dependent DNAzyme. Subsequent catalytic cleavage of the DNAzyme by the corresponding metal ions results in recycling of the enzymatic sequences and cyclic cleavage of the substrate strand, liberating many short FAM-linked oligonuleotide fragments separated from the GO surface, which results in fluorescence enhancement due to the weak affinity of the short FAM-linked oligonuleotide fragment to GO. The amount of produced short FAM-linked oligonuleotide fragments is positively related to the concentration of ATP. This means that one target binding could result in cleaving multiplex fluorophore labelled substrate strands, which provided effective signal amplification. The vivo studies suggested that the nanoprobe was efficiently delivered into living cells and worked for specific, high-contrast imaging of target ATP. More importantly, this target-responsive nanoscissor model is an important approach for intracellular amplified detection and imaging of various analytes by selecting appropriate affinity ligands.

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mentioning

confidence: 99%

Proximity hybridization triggered strand displacement and DNAzyme assisted strand recycling for ATP fluorescence detection in vitro and imaging in living cells

Gao

Yao

et al. 2018

RSC Adv.

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“…Surprisingly, the amount of background noise in absence of ST (Leak II) was overwhelmingly high and accounted for 56.5% of the positive signal. This was in spite of using one particular combination of association region length (6 nt) and toehold length (9 nt) previously reported by Le's group to give minimal background noise (nt = nucleotide) (17). This may be due to the significantly higher probe concentration (100 n M versus 10 n M ) or different reaction buffer used in this study.…”

Section: Resultsmentioning

confidence: 85%

“…An association region was also incorporated to thermodynamically stabilize the intermediate I1–I2 complex (16). The application of such DNA three-way junctions for protein detection was recently demonstrated by Le's group (17–19). …”

Section: Introductionmentioning

confidence: 99%

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Engineering a robust DNA split proximity circuit with minimized circuit leakage

Ang¹,

Tong²,

Yung³

2016

Nucleic Acids Res

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DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically analyzed the sources and characteristics of various types of leakage in a split proximity circuit which was engineered to spatially probe for target sites held within close proximity. Direct evidence that 3′-truncated oligonucleotides were the major impurity contributing to circuit leakage was presented. More importantly, a unique strategy of translocating a single nucleotide between domains, termed ‘inter-domain bridging’, was introduced to eliminate toehold-independent leakages while enhancing the strand displacement kinetics across a three-way junction. We also analyzed the dynamics of intermediate complexes involved in the circuit computation in order to define the working range of domain lengths for the reporter toehold and association region respectively. The final circuit design was successfully implemented on a model streptavidin-biotin system and demonstrated to be robust against both circuit leakage and biological interferences. We anticipate that this simple signal transduction strategy can be used to probe for diverse biomolecular interactions when used in conjunction with specific target recognition moieties.

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“…This technique makes use of the attractive properties of nucleic acids for desired signal transduction and amplification [81,82]. For example, Landegren et al [83] combined proximity ligation assay (PLA) using DNA-bound antibodies to recognize the target molecule with RCA amplification to develop a method for highly sensitive protein detection.…”

Section: Proximity Ligation For Amplified Immunoassaymentioning

confidence: 99%

Signal Amplification for Highly Sensitive Immunosensing

2017

J. Anal. Test.

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To dissolve the bottleneck problem of life and biomedical science in detection of biomolecules with low abundance and acquisition of ultraweak biological signals, highly sensitive analytical methods coupling with the specificity of biological recognition events have been quickly developed by the exploring of signal amplification strategies. These strategies have extensively been introduced into the development of highly sensitive immunosensing methods by combining with highly specific immunological recognition. They can be divided into two groups. One group of strategies attempts to transfer the immunological recognition event into large number of reporter probes or signal probes for signal readout by employing nano/micro-materials as vehicles for multi-labeling and/or molecular biological amplification for increasing the abundance of the signal molecules. The other uses nanomaterials or enzyme mimics as catalytic tools/tags to obtain enhanced detection signal. This review focuses on the significant advances in design of signal amplification strategies for highly sensitive immunosensing.

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Binding-Induced Formation of DNA Three-Way Junctions and Its Application to Protein Detection and DNA Strand Displacement

Cited by 86 publications

References 28 publications

Proximity hybridization triggered strand displacement and DNAzyme assisted strand recycling for ATP fluorescence detection in vitro and imaging in living cells

Proximity hybridization triggered strand displacement and DNAzyme assisted strand recycling for ATP fluorescence detection in vitro and imaging in living cells

Engineering a robust DNA split proximity circuit with minimized circuit leakage

Signal Amplification for Highly Sensitive Immunosensing

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