A Highly Sensitive, Excimer‐Controlled Molecular Beacon

Häner, Robert; Biner, Sarah M.; Langenegger, Simon M.; Meng, Tao; Malinovskii, Vladimir L.

doi:10.1002/ange.200905829

Cited by 58 publications

(51 citation statements)

References 64 publications

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“…Additionally, MB should not take part in unintended target hybridization, which might affect selectivity, or interfere with formation of the hairpin structure, for example by binding to the stem sequence, which may also lead to an increase in background or loss of signal intensity. To avoid incomplete FRET or quenching in a hairpin form, Haner et al reported MB design in which signal control is accomplished by formation of a donor–acceptor (D–A) complex [86]. The stem contains incorporated pairs of pyrene or perylenediimide moieties that can interact by interstrand stacking.…”

Section: Hybridization Probesmentioning

confidence: 99%

Nucleic acid-based fluorescent probes and their analytical potential

2010

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It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.FigureHybridization with a nucleic acid target or affinity interactions with a nonnucleic acid target generate changes in the fluorescence characteristics of a nucleic acid-based fluorescent probe

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Section: Hybridization Probesmentioning

confidence: 99%

Nucleic acid-based fluorescent probes and their analytical potential

2010

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“…[11][12][13] Hence, it is not surprising that this chromophore has been extensively applied in the construction of aggregates inside and outside of double-helical DNA. [11][12][13][14][15][16][17][18][19][20] PBI derivatives have been covalently attached to oligonucleotides for the DNA-directed assembly of this dye in thermophilic foldamers, [14,15] as caps that trigger the aggregation of DNA hairpins, [16,17] for the construction of exceptionally stable triplexes, [11,18] for electron-transfer studies, [19] and for fluorescence quenching in highly sensitive molecular beacons. [20] For the incorporation of PBI as an artificial base surrogate at both internal and terminal positions in DNA, we recently presented a synthetic protocol based on automated phosphoramidite building block chemistry.…”

Section: Introductionmentioning

confidence: 99%

Assembly of DNA Triangles Mediated by Perylene Bisimide Caps

Menacher

Stepanenko

Würthner

et al. 2011

Chemistry A European J

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Perylene bisimides (PBI) have been synthetically incorporated as caps onto a Y-shaped DNA triple strand. These PBI caps serve as "sticky" ends in the spontaneous assembly of larger DNA ensembles, linking the triangular DNA through stacking interactions. This, in turn, yields a hypsochromic shift in the absorption and a red shift in the fluorescence as characteristic optical readouts. This assembly occurs spontaneously without any enzymatic ligation process and without the use of overhanging DNA as sticky ends. Instead, dimerizations of the PBI chromophores in the assembly are controlled by the DNA as a structural scaffold. Thereby, the PBI-driven assembly is fully reversible. Due to the fact that PBI dimerization does not occur in the single strand, the aggregates can be destroyed by thermal dehybridization of the DNA scaffold and reassembled by reannealing of the DNA construct. In view of the fact that PBI forms stable radical anions, the presented DNA architectures are not only interesting optical biomaterials, but are also promising materials for molecular electronics with DNA.

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“…Zhang and Winfree have shown that single-nucleotide mutations, insertions, and deletions in the catalyst strand can result in 10-to 300-fold reductions in its efficiency in catalyzing strand exchange [17]. These reductions in signal observed with single-nucleotide mismatches are comparable to other well-developed DNA sensors [26][27][28][31][32][33]. Consistent with these findings, we observed that when a single nucleotide was changed in the toehold region (Figure 3, inset), the mutant Trigger did not yield any peroxidase activity above background even at 150 nM concentration ( Figure 3, sample #10~12).…”

Section: Resultsmentioning

confidence: 86%

Beyond allostery: Catalytic regulation of a deoxyribozyme through an entropy-driven DNA amplifier

et al. 2010

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The programmability and replicability of RNA and DNA have respectively enabled the design and selection of a number of allosteric ribozymes and deoxyribozymes. These catalysts have been adapted to function as signal transducers in biosensors and biochemical reaction networks both in vitro and in vivo. However, allosteric control of nucleic acid catalysts is currently limited by the fact that one molecule of effector (input) generally regulates at most one molecule of ribozyme or deoxyribozyme (output). In consequence, allosteric control is usually inefficient when the concentration of input molecules is low. In contrast, catalytic regulation of protein enzymes, as in protein phosphorylation cascades, generally allows one input molecule (e.g., one kinase molecule) to regulate multiple output molecules (e.g., kinase substrates). Achieving such catalytic signal amplification would also be of great utility for nucleic acid circuits. Here we show that allosteric regulation of nucleic acid enzymes can be coupled to signal amplification in an entropy-driven DNA circuit. In this circuit, kinetically trapped DNA logic gates are triggered by a specific sequence, and upon execution generate a peroxidase deoxyribozyme that converts a colorless substrate (ABTS) into a green product (ABTS •+). This scheme provides a new paradigm for the design of enzyme-free biosensors for point-of-care diagnostics. FindingsA variety of functional nucleic acids have been engineered over the past two decades, including not only simple binding elements (aptamers [1,2]) and catalysts (ribozymes [3] and deoxyribozymes [4]), but also more 'intelligent' molecular parts, such as aptamer beacons and allosteric ribozymes that can sense biomolecules [5,6], process molecular information [7,8], and regulate biochemical systems [9]. However, most regulatory nucleic acid elements are based on allosteric control, which has a fundamental limitation: one input molecule generally yields only one output molecule. Such stoichiometric or sub-stoichiometric regulation is often insufficient for effective metabolic regulation or diagnostic signal transduction, especially when the concentrations of input molecules are low.In contrast, natural catalytic cascades, such as the phosphorylation of proteins by kinases, readily amplify low input signals. Although in principle ribozymes and deoxyribozymes could participate in similar cascades as catalysts [10][11][12], no generalizable method for implementing such cascades has yet been established. On the other hand, DNA and RNA can catalyze chemical reactions not only by forming intricate tertiary structures, but also by simply forming Watson-Crick base pairs. In fact, by serving as a hybridization template, DNA can control and catalyze a wide range of chemical reactions [13], some of which can yield products capable of regulating downstream reactions. More recently, Zhang and coworkers have designed a scheme for highly efficient, enzyme-free, entropy-driven catalytic reactions that relies only on the dynamic hybrid...

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A Highly Sensitive, Excimer‐Controlled Molecular Beacon

Cited by 58 publications

References 64 publications

Nucleic acid-based fluorescent probes and their analytical potential

Nucleic acid-based fluorescent probes and their analytical potential

Assembly of DNA Triangles Mediated by Perylene Bisimide Caps

Beyond allostery: Catalytic regulation of a deoxyribozyme through an entropy-driven DNA amplifier

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