An electrochemical impedance sensor for simple and specific recognition of G–G mismatches in DNA

Huang, Min; Li, Hanying; He, Hanping; Zhang, Xun; Wang, Shengfu

doi:10.1039/c6ay01705c

Cited by 18 publications

(7 citation statements)

References 49 publications

(41 reference statements)

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“…Two gaps were observed in the Figure 4 a; none of the NBP

and UBP

has a N–H⋯N bond in the BSO n range between 0.385 and 0.397 and between 0.426 and 0.455. One of the UBP

with the strongest N–H⋯N bonds, the GG base pair with a BSO n value of 0.426 has been discussed in so-called mismatched DNA causing genetic diseases [ 137 , 138 ]. The GG base pair has also the capability to form a H-bonding pattern close to that found in NBP

, i.e., being stabilized by three HBs, N–H⋯N, N–H⋯O and C–H⋯O (see Figure 2 ) making this pair an interesting candidate for xenobiology [ 33 , 34 , 139 ].…”

Section: Results and Discussionmentioning

confidence: 99%

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

2021

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In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)–thymine (T), adenine (A)–uracil (U) and guanine (G)–cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N–H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O–H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C–H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C–H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N–H⋯N bond and the C–H⋯O bonds, and at the same time decreases the strength of the N–H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

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“…Two gaps were observed in the Figure 4 a; none of the NBP

and UBP

has a N–H⋯N bond in the BSO n range between 0.385 and 0.397 and between 0.426 and 0.455. One of the UBP

, i.e., being stabilized by three HBs, N–H⋯N, N–H⋯O and C–H⋯O (see Figure 2 ) making this pair an interesting candidate for xenobiology [ 33 , 34 , 139 ].…”

Section: Results and Discussionmentioning

confidence: 99%

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

2021

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“…In addition, an electrochemical biosensor based on EIS provides several benefits such as low power consumption, and ease of miniaturization. EIS biosensors provides signal out-put by using periodic small AC perturbations and responds to signal change caused by the binding of bio-analytes to the immobilized bio-recognition elements on the electrode surface [ 38 ]. Due to these advantages an impedance based biosensor finds a suitable position compared to the other electrochemical transduction mechanisms for developing miniaturized point-of-care-testing (POC) applications.…”

Section: Introductionmentioning

confidence: 99%

Electrochemical Immunosensor for the Early Detection of Rheumatoid Arthritis Biomarker: Anti-Cyclic Citrullinated Peptide Antibody in Human Serum Based on Avidin-Biotin System

Chinnadayyala

Cho

2020

Sensors

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Rheumatoid arthritis (RA) is a chronic autoimmune disease that produces a progressive inflammatory response that leads to severe pain, swelling, and stiffness in the joints of hands and feet, followed by irreversible damage of the joints. The authors developed a miniaturized, label-free electrochemical impedimetric immunosensor for the sensitive and direct detection of arthritis Anti-CCP-ab biomarker. An interdigitated-chain-shaped microelectrode array (ICE) was fabricated by taking the advantage of microelectromechanical systems. The fabricated ICE was modified with a self-assembled monolayer (SAM) of Mercaptohexanoic acid (MHA) for immobilization of the synthetic peptide bio-receptor (B-CCP). The B-CCP was attached onto the surface of SAM modified ICE through a strong avidin-biotin bio-recognition system. The modified ICE surface with the SAM and bio-molecules (Avidin, B-CCP, Anti-CCP-ab and BSA) was morphologically and electrochemically characterized. The change in the sensor signal upon analyte binding on the electrode surface was probed through the electrochemical impedance spectroscopy (EIS) property of charge-transfer resistance (Rct) of the modified electrodes. EIS measurements were target specific and the sensor response was linearly increased with step wise increase in target analyte (Anti-CCP-ab) concentrations. The developed sensor showed a linear range for the addition of Anti-CCP-ab between 1 IU mL−1 → 800 IU mL−1 in phosphate buffered saline (PBS) and Human serum (HS), respectively. The sensor showed a limit of detection of 0.60 IU mL−1 and 0.82 IU mL−1 in the PBS and HS, respectively. The develop bio-electrode showed a good reproducibility (relative standard deviation (RSD), 1.52%), selectivity and stability (1.5% lost at the end of 20th day) with an acceptable recovery rate (98.0% → 101.18%) and % RSD’s for the detection of Anti-CCP-ab in spiked HS samples.

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“…Although (unbiased) charge transfer in DNA nearly vanishes after 10 to 20 nm [8][9][10], DNA is still a promising component for (biased) charge transport in molecular electronics, e.g., as a short molecular wire [11]. It may also be exploited in nanotechnology for nanosensors [12] and molecular wires [13,14].…”

Section: Introductionmentioning

confidence: 99%

RT-TDDFT study of hole oscillations in B-DNA monomers and dimers

et al. 2017

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We employ Real-Time Time-Dependent Density Functional Theory to study hole oscillations within a B-DNA monomer (one base pair) or dimer (two base pairs). Placing the hole initially at any of the bases which make up a base pair, results in THz oscillations, albeit of negligible amplitude. Placing the hole initially at any of the base pairs which make up a dimer is more interesting: For dimers made of identical monomers, we predict oscillations with frequencies in the range f ≈ 20-80 THz, with a maximum transfer percentage close to 1. For dimers made of different monomers, f ≈ 80-400 THz, but with very small or small maximum transfer percentage. We compare our results with those obtained recently via our Tight-Binding approaches and find that they are in good agreement.

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An electrochemical impedance sensor for simple and specific recognition of G–G mismatches in DNA

Abstract: A simple EIS sensor was developed for the highly sensitive and specific detection of G–G mismatches in dsDNA using a small molecule-modified gold electrode. Recognition and detection were achieved by ΔRct before and after incubation with target DNA.

Cited by 18 publications

References 49 publications

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

Electrochemical Immunosensor for the Early Detection of Rheumatoid Arthritis Biomarker: Anti-Cyclic Citrullinated Peptide Antibody in Human Serum Based on Avidin-Biotin System

RT-TDDFT study of hole oscillations in B-DNA monomers and dimers

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