Molecular Engineering of DNA: Molecular Beacons

Wang, Kemin; Tang, Zhixiang; Yang, Chaoyong; Kim, Youngmi; Fang, Xiaohong; Li, Wei; Wu, Yanrong; Medley, Colin D.; Cao, Zehui; Li, Jun; Colon, Patrick; Lin, Hui; Tan, Weihong

doi:10.1002/anie.200800370

Cited by 606 publications

(388 citation statements)

References 156 publications

(245 reference statements)

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“…The hairpin is initially closed to give low fluorescence. A target DNA opens up the hairpin to increase the distance between the fluorophore and quenching, leading to signal increase [85]. Molecular beacons are attractive analytical probes since they allow for simple homogeneous assays with high sensitivity.…”

Section: Molecular Beaconsmentioning

confidence: 99%

DNA-stabilized, fluorescent, metal nanoclusters for biosensor development

Liu

2014

TrAC Trends in Analytical Chemistry

198

141

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In the past decade, fluorescent silver, gold and copper nanoclusters (Ag, Au and CuNCs) have emerged as a new class of signaling moiety for biosensor development. Compared to semiconductor quantum dots, metal NCs have less toxicity concerns and can be more easily conjugated to biopolymers. Due to their extremely small size, these NCs need a stabilizing ligand. Many polymers, proteins and nucleic acids have been reported to stabilize NCs. In particular, many DNA sequences produce highly fluorescence NCs. Coupling these DNA stabilizers with other sequences such as aptamers has generated a large number of biosensors. In this review, the synthesis of DNA and nucleotide-templated NCs is first summarized; their chemical interactions are also discussed. In the second part, the properties of NCs such as fluorescence quantum yield, emission wavelength and lifetime, structure and photostability are briefly reviewed. In the last part, various sensor design strategies using these NCs are categorized into the following four classes: 1) fluorescence de-quenching; 2) generation of templating DNA sequences to produce NCs; 3) change of nearby environment; and 4) reacting with heavy metal ions or other quenchers. Finally, the future trends in this field are discussed.

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Section: Molecular Beaconsmentioning

confidence: 99%

DNA-stabilized, fluorescent, metal nanoclusters for biosensor development

Liu

2014

TrAC Trends in Analytical Chemistry

198

141

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“…Because the sequences of aptamer probes can be custom-designed, aptamers have the particular advantage of target recognition-triggered conformational alteration, leading, in turn, to signal alteration. This strategy has been well demonstrated with molecular beacons for nucleic acid monitoring and free protein detection (22,23). Assuming that this strategy would work on surface membrane proteins of living cancer cells, we hypothesized that conformational alteration triggered by the specific binding of aptamers with cell membrane proteins could detect cancer cells, thus affording a substantial basis for the development of a unique kind of activatable molecular probe for in vivo cancer imaging.…”

mentioning

confidence: 99%

Activatable aptamer probe for contrast-enhanced in vivo cancer imaging based on cell membrane protein-triggered conformation alteration

Shi

He²,

Wang³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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285

227

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Aptamers have emerged as promising molecular probes for in vivo cancer imaging, but the reported "always-on" aptamer probes remain problematic because of high background and limited contrast. To address this problem, we designed an activatable aptamer probe (AAP) targeting membrane proteins of living cancer cells and achieved contrast-enhanced cancer visualization inside mice. The AAP displayed a quenched fluorescence in its free state and underwent a conformational alteration upon binding to target cancer cells with an activated fluorescence. As proof of concept, in vitro analysis and in vivo imaging of CCRF-CEM cancer cells were performed by using the specific aptamer, sgc8, as a demonstration. It was confirmed that the AAP could be specifically activated by target cancer cells with a dramatic fluorescence enhancement and exhibit improved sensitivity for CCRF-CEM cell analysis with the cell number of 118 detected in 200 μl binding buffer. In vivo studies demonstrated that activated fluorescence signals were obviously achieved in the CCRF-CEM tumor sites in mice. Compared to always-on aptamer probes, the AAP could substantially minimize the background signal originating from nontarget tissues, thus resulting in significantly enhanced image contrast and shortened diagnosis time to 15 min. Furthermore, because of the specific affinity of sgc8 to target cancer cells, the AAP also showed desirable specificity in differentiating CCRF-CEM tumors from Ramos tumors and nontumor areas. The design concept can be widely adapted to other cancer cell-specific aptamer probes for in vivo molecular imaging of cancer.switchable aptamer probe | in vivo imaging | activatable fluorescent molecular imaging | cancer detection | cell surface protein

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“…Moreover the use of Au based quenching has been shown to be characterised by minimal background fluorescence and subsequently improved signal-tobackground ratio (9,23,26).…”

Section: Introductionmentioning

confidence: 99%

“…The first report on the use of AuNPs as quenchers in MB and their application for the detection of specific DNA sequence was presented by Dubertret et al (19), where the authors demonstrated the possibility of replacing the quencher in a MB with AuNPs. Following this first report other authors investigated the use of MBs-AuNPs for the detection of genetic disease (12) demonstrating the ability to discriminate single point mismatches (26,30). Significant improvement in the state-of-the-art was achieved by Song et al (9) where the authors, by taking fully advantage of the quenching efficiency and scaffolding ability of AuNPs, demonstrated the possibility of having three perfectly and independently working molecular beacons immobilised on a single AuNPs highlighting the possibility of single particle multiplex detection of DNA markers.…”

Section: Introductionmentioning

confidence: 99%

Gold nanoparticle fluorescent molecular beacon for low-resolution DQ2 gene HLA typing

et al. 2011

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Coeliac disease is an inflammation of the small intestine triggered by gluten ingestion. Herein we present a fluorescent genosensor, exploiting molecular beacons functionalised gold nanoparticle, for the identification of Human Leukocyte Antigens (HLA) DQ2 gene, a key genetic factor in coeliac disease.Optimisation of sensor performance was achieved by tuning the composition of the oligonucleotide monolayer immobilised on the Au nanoparticle and the molecular beacon design.Co-immobilisation of the molecular beacon with a spacing oligo (thiolated 10-Thymines oligo) in the presence of 10 Adenines oligos, resulted in a significant increase of sensor response due to improved spacing of the molecular beacons and extension from the nanoparticle surface ,which renders them more available for recognition.Further increase in response (ca. 40%) was shown to be achievable when the recognition sequence of the molecular beacon was incorporated in the stem. Improvement of the molecular beacons' specificity was also achieved by the incorporation within their recognition sequence of a one-base mismatch. Finally, a gold nanoparticle functionalised with two molecular beacons targeting the DQA1*05* and DQB1*02* alleles has been demonstrated to allow the low resolution typing of the DQ2 gene at nanomolar level.

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Molecular Engineering of DNA: Molecular Beacons

Cited by 606 publications

References 156 publications

DNA-stabilized, fluorescent, metal nanoclusters for biosensor development

DNA-stabilized, fluorescent, metal nanoclusters for biosensor development

Activatable aptamer probe for contrast-enhanced in vivo cancer imaging based on cell membrane protein-triggered conformation alteration

Gold nanoparticle fluorescent molecular beacon for low-resolution DQ2 gene HLA typing

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