Probing structural changes of self assembled i-motif DNA

Lee, Il Joon; Patil, Sachin P.; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

doi:10.1039/c4cc06824f

Cited by 56 publications

(37 citation statements)

References 53 publications

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“…59 At present, the G-quadruplex specific ThT has attracted increasing interests, and it has been used as a light-up fluorescence probe for the sensing of the G-quadruplex, biothiols, Hg 2+ , K + , liver-related short gene, and the structure change of i-moif. [60][61][62][63][64][65] Inspired by these studies, we constructed a new FRET system using CP as an donor and ThT as an acceptor, and designed a simple, label-free, and sensitive biosensor for the detection of thrombin in buffer and in diluted serum. An improved sensitivity for thrombin detection was obtained when compared with two recent strategies based on the FRET from the CP to the dye.…”

mentioning

confidence: 99%

Thioflavin T as an Efficient G-Quadruplex Inducer for the Highly Sensitive Detection of Thrombin Using a New Föster Resonance Energy Transfer System

Liu

Hua

Fan

et al. 2015

ACS Appl. Mater. Interfaces

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We report a new Föster resonance energy transfer (FRET) system that uses a special dye, thioflavin T (ThT), as an energy acceptor and a water-soluble conjugated polymer (CP) with high fluorescence as an energy donor. A simple, label-free, and sensitive strategy for the detection of thrombin in buffer and in diluted serum was designed based on this new system using ThT as an efficient inducer of the G-quadruplex. The difference between the blank and the positive samples was amplified due to distinctive FRET signals because thrombin has little effect on the intercalation of ThT into the G-quadruplex. In the absence of the target, ThT induces the aptamer to form a G-quadruplex and intercalates into it with strong fluorescence. The electrostatic attractions between the negatively charged G-quadruplex and positively charged CP allow a short donor-acceptor distance, resulting in a high FRET signal. However, in the presence of the target, the aptamer forms a G-quadruplex-thrombin complex first, followed by the intercalation of ThT into the G-quadruplex. A long distance exists between the donor and acceptor due to the strong steric hindrance from the large-sized thrombin, which leads to a low FRET signal. Compared with previously reported strategies based on the FRET between the CP and dye, our strategy is label-free, and the sensitivity was improved by an order of magnitude. Our strategy also shows the advantages of being simple, rapid (about 50 min), sensitive, label-free, and low-cost in comparison to strategies based on the FRET between quantum dots and dyes.

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confidence: 99%

Thioflavin T as an Efficient G-Quadruplex Inducer for the Highly Sensitive Detection of Thrombin Using a New Föster Resonance Energy Transfer System

Liu

Hua

Fan

et al. 2015

ACS Appl. Mater. Interfaces

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“…The i-motif structure can be induced and consolidated by a slightly acidic pH (protonation of the N3 in cytosine) or Ag + at neutralp H( formation of C-Ag + -C), so that basic logic gates could be easily operated by inputting ap Hm odulated factor or Ag + affinity agents, such as cysteineo rh alide ions. Similar to G-quadruplexes, many fluorescent dyes have been reported that have the capability of binding i-motif with enhanced luminescent signals,s uch as [Ru(phen) 2 (dppz)] 2 + , [80] crystal violet, [81] ThT, [82] cyanine dye DMSB, [83] thiazole orange (TO), [84] and berberine, [85] which provide i-motif-based circuits with detectable outputs. [86] For instance, Ta ng et al [87] designed aC -rich strand to realize OR and INHIBIT functions by employing Ag + /H + and Ag + /I À as the inputs, respectively and DMSB as the signal actuator.L uo et al [84b] took TO as i-motif monitor and Ag + /cysteine as inputs to operate an INHIBIT gate.…”

Section: Signalwith the Help Of I-motifmentioning

confidence: 99%

Recent Progress in Fluorescence Signal Design for DNA‐Based Logic Circuits

Yang

Song

et al. 2019

Chemistry A European J

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DNA‐based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA′s advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA‐based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA‐based logic circuit construction. Although work on sequence and structure design for DNA‐based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA‐based logic circuits. Several basic strategies are summarized and a few designs for developing multi‐output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.

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“…In 2015, ThT was employed as fluorescence sensor for detection of imotif in retinoblastoma (Rb) and RET proto-oncogene using CD spectroscopy and fluorescence studies at different pH values. It was found that ThT acted as an efficient sensor to probe the conformational changes in i-motifs by the virtue of its high degree of sensitivity towards changes in its local microenvironment (Lee et al, 2015).…”

Section: Thioflavin-t: Nucleic Acid Sensormentioning

confidence: 99%