Colorimetric detection of clinical DNA samples using an intercalator-conjugated polydiacetylene sensor

Jung, Yun Kyung; Park, Hyun Gyu

doi:10.1016/j.bios.2015.04.093

Cited by 43 publications

(11 citation statements)

References 24 publications

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“…A linear relationship between the relative fluorescence change at 640 nm and the concentration of target miRNA-21(0-20 nM) was observed, indicating that above microtube could be applied to accurately detect the concentration of target miRNA-21 in aqueous solution (Figure 3d). The detection limit (3σ/slope) was about 2 nM, which is comparable to that of the PDA vesicle sensor system [30]. However, the present detection limit was still far higher than the typical levels of miRNA in serum, and further efforts should be made to enhance the sensitivity of PDA based sensor system.…”

Section: Resultsmentioning

confidence: 80%

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Selective and sensitive detection of MiRNA-21 based on gold-nanorod functionalized polydiacetylene microtube waveguide

Zhu

Qiu

Yang

et al. 2016

Biosensors and Bioelectronics

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Section: Resultsmentioning

confidence: 80%

“…A variety of PDA based liposome or vesicle probes have been utilized to detect oligonucleotides, double-stranded DNA or single-stranded DNA (ss-DNA) [30], liver cancer biomarkers and so on [31]. However, some limitations, including low stability and selectivity, the inability for precise quantitative analysis, limited their practical applications.…”

mentioning

confidence: 99%

Selective and sensitive detection of MiRNA-21 based on gold-nanorod functionalized polydiacetylene microtube waveguide

Zhu

Qiu

Yang

et al. 2016

Biosensors and Bioelectronics

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“…This provides the increase of head group area and the decrease in the packing parameter, leading to the differences in molecular organization and ultimately different shape and size of poly(PCDA)/Neo-PCDA assembly. 39,77–78 Jung 66,79 , Cheng 80 and Ye 81 also demonstrate that the variation of head group structure provides different shape and size of PDA assemblies. Flower-like morphology, rectangular shape, fiber, ribbon with various size in the range of nanometer to micrometer are observed.…”

Section: Resultsmentioning

confidence: 93%

“…29,30 PDA possesses color transition, typically from blue to red, upon the exposure to various external stimuli such as heat, 31–42 acids and bases, 40,43–46 chemicals 47–56 and biomolecules. 57–66 The perturbation by these stimuli generally weakens segmental interactions within the PDA assemblies. This results in the reorientation of conjugated backbone and alkyl chain.…”

Section: Introductionmentioning

confidence: 99%

Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA

et al. 2017

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Recognition of nucleic acids remains an important endeavor in biology. Nucleic acids adopt shapes ranging from A-form (RNA and GC rich DNA) to B-form (AT rich DNA). We show, in this contribution, shape-specific recognition of A-U rich RNA duplex by a neomycin (Neo)-polydiacetylene (PDA) complex. PDA assemblies are fabricated by using a well-known diacetylene (DA) monomer, 10,12-pentacosadiynoic acid (PCDA). The response of poly(PCDA) assemblies is generated by mixing with a modified neomycin-PCDA monomer (Neo-PCDA). The functionalization by neomycin moiety provides specific binding with homopolyribonucleotide poly (rA) - poly (rU) stimulus. Various types of alcohols are utilized as additives to enhance the sensitivity of poly(PCDA)/Neo-PCDA assemblies. A change of absorption spectra is clearly observed when a relatively low concentration of poly (rA)-poly (rU) is added into the system. Furthermore, poly(PCDA)/Neo-PCDA shows a clear specificity for poly (rA)-poly (rU) over the corresponding DNA duplex. The variation of linker between neomycin moiety and conjugated PDA backbone is found to significantly affect its sensitivity. We also investigate other parameters including the concentration of Neo-PCDA and the DA monomer structure. Our results provide here preliminary data for an alternative approach to improve the sensitivity of PDA utilized in biosensing and diagnostic applications.

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“…Drug and DNA molecules experience certain modifications such that DNA conformation is mostly reversible for non-covalent interactions, which could be divided into three main groups: electrostatic binding, intercalation and groove binding (major and minor grooves) [4]. Electrostatic binding occurs due to interaction between the negatively charged phosphate backbone of DNA and the positively charged ends of small molecules.…”

Section: Introductionmentioning

confidence: 99%

Determination of Electrochemical Interaction between 2‐(1H‐benzimidazol‐2‐yl) Phenol and DNA Sequences

Topkaya

Çetin

2019

Electroanalysis

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A benzimidazole derivate, 2‐(1H‐benzimidazol‐2‐yl) phenol (2‐Bip) and its interaction mechanism with sequence specific DNA was examined with Differential Pulse Voltammetry (DPV). We, for the first time, investigated the effect of 2‐Bip on sequence specific DNA with electrochemical methods by evaluating both guanine and 2‐Bip oxidation signal changes. In the study, probe sequences were immobilized to the surface of the electrodes and then hybridization was achieved by sending the complementary target onto the probe modified electrodes. Following the hybridization, 2‐Bip solution was interacted with probe and hybrid sequences to see the effect of 2‐Bip on different DNA sequences. The binding constant (K), toxicity (S%) and thermodynamic parameters, i. e., Gibbs free energy (ΔG°) of 2‐Bip‐DNA complexes were evaluated. K was calculated as 5×105 and the change in the ΔG° was found as −32.50 kJ mol−1, which are consistent well with the literature. Furthermore, S% showed that 2‐Bip is moderately toxic to single stranded DNA (ssDNA) and toxic to double stranded DNA (dsDNA). From our experimental data, we made four conclusions (i) 2‐Bip affects both ssDNA and dsDNA, (ii) 2‐Bip interaction mode with DNA could be non‐covalent interactions, (iii) 2‐Bip could be used as new DNA hybridization indicator due to its distinct effects on ssDNA and dsDNA, (iv) 2‐Bip could be used as a drug molecule for its DNA effect.

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Colorimetric detection of clinical DNA samples using an intercalator-conjugated polydiacetylene sensor

Cited by 43 publications

References 24 publications

Selective and sensitive detection of MiRNA-21 based on gold-nanorod functionalized polydiacetylene microtube waveguide

Selective and sensitive detection of MiRNA-21 based on gold-nanorod functionalized polydiacetylene microtube waveguide

Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA

Determination of Electrochemical Interaction between 2‐(1H‐benzimidazol‐2‐yl) Phenol and DNA Sequences

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