Sandwich probes: two simultaneous reactions for templated nucleic acid detection

Kleinbaum, Daniel J.; Kool, Eric T.

doi:10.1039/c0cc01968b

Cited by 24 publications

(9 citation statements)

References 15 publications

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“…[29][30][31][32] This technology has been applied to SNP detection. [33][34][35][36][37][38][39] However, as for any binary probe detection, 40 there is a delicate trade-off between sensitivity and single nucleotide resolution; the longer the probes, the better the detection threshold but the lower the resolution. In templated reactions, this must be further balanced with amplication; the longer the probe, the slower the template turn-over (amplication).…”

Section: Introductionmentioning

confidence: 99%

“…46 The choice of this reaction was based on its fast kinetics, its biorthogonality 47 and the fact that the guide DNAs do not need to exchange on the template in order to achieve amplication. While a templated reaction with sandwich probes has been reported, 37 it explored the benet of a double ligation reaction to suppress the background signal arising from the hydrolysis of a labile quencher. Since two reactions are required to remove the quenchers, the signal to noise ratio of detection was improved.…”

Section: Introductionmentioning

confidence: 99%

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Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

Kim

Winssinger

2020

Chem. Sci.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

Kim

Winssinger

2020

Chem. Sci.

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“…OTRs rely upon sequence‐specific Watson–Crick base‐pairing to bring together two reactive moieties (or probe‐heads), each attached to the end of an oligonucleotide (or oligonucleotide analogue) strand (Scheme ) . Because of their intrinsic specificity and high programmability, OTRs have found valuable applications in controlled organic synthesis, DNA‐encoded chemistry for drug discovery, and nucleic acid (NA) sensing both in vitro,, and in vivo . For sensing applications, OTRs were successfully engineered whereby only the NA target of interest acts as a template to catalyze an otherwise highly unfavorable reaction, which can be monitored optically (for example, changes in fluorescence intensity and/or wavelength).…”

Section: Methodsmentioning

confidence: 99%

Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity

2017

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Oligonucleotide-templated reactions are valuable tools for nucleic acid sensing both in vitro and in vivo.They are typically carried out under conditions that make any reaction in the absence of template highly unfavorable (most commonly by using alow concentration of reactants), whichhas anegative impact on the detection sensitivity.H erein, we report an ovel platform for fluorogenic oligonucleotide-templated reactions between peptide nucleic acid probes embedded within permeable agarose and alginate hydrogels.W ed emonstrate that under conditions of restricted mobility (that is,l imited diffusion), non-specific interactions between probes are prevented, thus leading to lower background signals.W hen applied to nucleic acid sensing, this accounts for as ignificant increase in sensitivity (that is,lower limit of detection). Optical nucleic acid sensors based on fluorogenic peptide nucleic acid probes embedded in permeable,p hysically crosslinked, alginate beads were also engineered and proved capable of detecting DNAconcentrations as low as 100 pm.Widely present in nature,m ost notably to catalyze phosphodiester bond formation in key biological processes including transcription and translation, oligonucleotide templated reactions (OTRs) are highly versatile and have been successfully applied to ab road range of chemistries.[1] This powerful concept allows unfavorable reactions between molecules present at very low concentrations to take place by increasing their effective concentration. OTRs rely upon sequence-specific Watson-Crick base-pairing to bring together two reactive moieties (or probe-heads), each attached to the end of an oligonucleotide (or oligonucleotide analogue) strand (Scheme 1).[1] Because of their intrinsic specificity and high programmability,O TRs have found valuable applications in controlled organic synthesis, [2] DNA-encoded chemistry for drug discovery, [3] and nucleic acid (NA) sensing both in vitro [1b,e,f,4] and in vivo.[5] For sensing applications,O TRsw ere successfully engineered whereby only the NA target of interest acts as at emplate to catalyze an otherwise highly unfavorable reaction, which can be monitored optically (for example,changes in fluorescence intensity and/or wavelength). In such cases,t he fluorescence intensity emitted by the product of the OTRi sd irectly proportional to the amount of NA target present, whilst only very low levels of background fluorescence can be detected in the absence of the template (leading to ahigh signal-to-noise ratio or S/N). Representative examples include the quenched auto-ligation (QUAL) [4b,5a,b] strategy in which an OTR causes the release of aq uencher molecule,r esulting in the restoration of the intrinsic fluorescence of an otherwise quenched nearby fluorophore.A nother common strategy uses an oligonucleotide template to catalyze the formation of af luorescent dye from two non-or weakly fluorescent precursors. [4c, 6] Some of the reactions most commonly used in such applications include ester hydrolyses, [7] nucleophi...

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“…[76] A further modification of this system was reported using two quencher residues per fluorophore-tagged DNA probe ( Figure 8). [77,78] As a result, the background fluorescence level in such a double-displacement system was decreased together with the influence of the non-templated loss of the quencher owing to its hydrolysis by external nucleophiles. Complete unquenching of the "sandwich probes" containing reactive groups on the 3' and 5' termini is possible only after reaction and using two different phosphorothioate probes hybridizing to the same template, up-and downstream.…”

Section: Application Of Templated Ligationmentioning

confidence: 99%

Reactions Templated by Nucleic Acids: More Ways to Translate Oligonucleotide‐Based Instructions into Emerging Function

2013

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The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.

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Sandwich probes: two simultaneous reactions for templated nucleic acid detection

Cited by 24 publications

References 15 publications

Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity

Reactions Templated by Nucleic Acids: More Ways to Translate Oligonucleotide‐Based Instructions into Emerging Function

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