A “turn-on” and proximity ligation assay dependent DNA tweezer for one-step amplified fluorescent detection of DNA

Yun, Wen; Zhu, Hanhong; Wang, Hong; Zhang, Lin; Wang, Ruiqi; Ha, Xia; Wang, Xingmin; Zhang, Jiafeng; Chen, Hong; Yang, Lizhu

doi:10.1016/j.saa.2020.119292

Cited by 9 publications

(2 citation statements)

References 31 publications

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“… 19 Leveraging the concept of activating DNA tweezers through proximity-based connectivity analysis, researchers have realized an innovative one-step amplification fluorescence detection method for DNA, successfully analyzing DNA in human serum. 20 Concerning miRNA detection, miRNA, originating from cellular expression, can also serve as markers for a variety of diseases. Given the significant impact of miRNA on disease progression and recovery, concentrations of miRNA have attracted substantial attention for their potential role in early diagnosis and subsequent treatment strategies.…”

Section: Introductionmentioning

confidence: 99%

Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios

Yao,

Liu,

Liu

et al. 2024

iScience

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Section: Introductionmentioning

confidence: 99%

Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios

Yao,

Liu,

Liu

et al. 2024

iScience

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“…Ultraspecific fluorescent probes have been proposed to detect concentrations of nucleic acids in the picomolar range without the use of amplification methods. − Such amplification-free strategies dramatically shorten the assay duration and allow for point-of-care diagnostic tests. Fluorescently modified nucleotides are often designed to preserve the properties of canonical nucleobases and consequently the ability to form hydrogen-bonded base pairing, as well as enzyme and protein recognition .…”

Section: Introductionmentioning

confidence: 99%

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

Hernández Bustos,

Martiny,

Bom Pedersen

et al. 2023

Anal. Chem.

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We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.

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Engineering Logic‐Gated i‐Motif/G‐Quadruplex (iG4) Hybrid Structures for DNA Nanotweezer‐Based Aptasensing

Dong,

Li,

Wang

et al. 2024

Analysis & Sensing

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Given high levels of both K+ and H+ in the tumor microenvironment, G‐quadruplex (G4) and i‐motif can in principle be utilized as two cooperative modules to build logic‐gated DNA nanodevices for microenvironment recognition and targeting. Combined use of G4 and i‐motif in DNA nanoassemblies, however, usually causes the uncontrolled DNA aggregation. To address this trouble, we well design a novel i‐motif/G‐quadruplex (iG4) hybrid structure that integrates two four‐stranded DNA helices in a folding topology, with a parallel mini‐duplex flanking at the 5’ end to provide a binding site for fluorescent ligands. This design enables that the folded and lighting‐up DNA structure is favored by H+ and K+ together, consistent with a two‐input AND gate behavior. We then employ the iG4 structure to guide a DNA nanotweezer that is clamped by an altered split ATP aptamer, which brings a proximity effect contributing to the proper folding of iG4 in slightly acidic microenvironments and enables the sensitive detection of endogenous ATP in cancer cell lysates.

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A “turn-on” and proximity ligation assay dependent DNA tweezer for one-step amplified fluorescent detection of DNA

Cited by 9 publications

References 31 publications

Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios

Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

Engineering Logic‐Gated i‐Motif/G‐Quadruplex (iG4) Hybrid Structures for DNA Nanotweezer‐Based Aptasensing

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