Deoxyribonucleic Acid Recognition Research Articles

Atomic layer deposited zinc oxide thin film on pencil graphite for DNA sensor applications

Atomic Layer Deposition (ALD) enables precise thin-film deposition on electrode substrates for electrochemical sensors. In this work, we present the first example of ALD grown zinc oxide (ZnO) deposition on pencil graphite surfaces for deoxyribonucleic acid (DNA) sensory applications, including its detection and DNA damage investigation. For DNA sensing studies, the use of highly productive materials is essential. In this context, the ZnO modified pencil graphite electrodes (ZnO/PGEs) exhibited good electrochemical properties that make them a suitable substrate. ZnO films were characterized using scanning electron microscopy (SEM), ultraviolet-visible (UV-Vis) spectroscopy, photoluminescence (PL), X-ray photoelectron spectroscopy (XPS), and electrochemical methods. The DNA recognition capability of the thin film coated electrodes was tested by using differential pulse voltammetry (DPV), which showed a linear response ranging from 1 mg L−1 to 200 mg L−1 based on the oxidation of guanine (G) with a limit of detection value (LOD) of 0.53 mg L−1 (n = 3). In addition to this, impedimetric monitoring of oxidative DNA damage was performed in the presence of copper(II)/hydrogen peroxide (Cu(II)/H2O2) reagents, and protection studies were conducted in the presence of ascorbic acid. ZnO thin film-based electrodes exhibited good sensor performance in terms of sensitivity, stability, and reproducibility.

Polypyrrole‐Based Nanohybrid Electrodes: Their Preparation and Potential Use for DNA Recognition and Paclitaxel Quantification

AbstractFabrication of conducting polymer networks based on polypyrrole/multi‐walled carbon nanotubes (PPy/MWCNTs) modified graphite electrodes that were achieved with a single‐step electropolymerization and potential use of these electrodes for deoxyribonucleic acid (DNA) recognition and anticancer drug (Paclitaxel, PTX) quantification were presented in the present work. PPy/MWCNTs nanohybrid PGEs were constructed in aqueous solution of pyrrole (Py) and MWCNTs using cyclic voltammetry (CV) and constant potential electrolysis. So‐formed electrodes were characterized with cyclic voltammetry and electrochemical impedance spectroscopy (EIS). Surface morphologies of the surfaces were investigated by scanning electron microscopy (SEM) studies. Bio‐application of the PPy/MWCNTs nanohybrid modified PGEs were accomplished by subjecting them to double‐stranded DNA (dsDNA) modification for direct DNA recognition and PTX determination. For the drug determination, interaction of DNA‐based electrodes with PTX was investigated. Detection limit was found as 1.55 x 10−8 M based on the changes in the oxidation of guanine base which made the proposed electrode convenient for clinical trials.

Beyond native deoxyribonucleic acid, templating fluorescent nanomaterials for bioanalytical applications: A review.

Due to its unique programmability, nanosized structure, and biocompatible properties, deoxyribonucleic acid (DNA) has attracted increasing attention for the construction of versatile nanostructures and nanomaterials. This review summarizes the recent developments in DNA-templated fluorescent nanomaterials, including DNA-stabilized quantum dots (QDs) and DNA-templated metal nanoclusters (NCs), as well as their applications in bioanalysis. These fluorescent nanomaterials not only have good fluorescence properties but also exhibit excellent performance in DNA recognition, which greatly expands the range of their bioanalytical applications. Finally, we discuss some current challenges and future work in this field, with the goal of further promoting the potential applications and developments of DNA-templated fluorescent nanomaterials in biochemical analysis.

DNA-supramolecule conjugates in theranostics.

The elegant properties of deoxyribonucleic acid (DNA), such as accurate recognition, programmability and addressability, make it a well-defined and promising material to develop various molecular probes, drug delivery carriers and theranostic systems for cancer diagnosis and therapy. In addition, supramolecular chemistry, also termed "chemistry beyond the molecule", is a promising research field that aims to develop functional chemical systems by bringing discrete molecular components together in a manner that invokes noncovalent intermolecular forces, such as hydrophobic interaction, hydrogen bonding, metal coordination, and shape or size matching. Thus, DNA-supramolecule conjugates (DSCs) combine accurate recognition, programmability and addressability of DNA with the greater toolbox of supramolecular chemistry. This review discusses the applications of DSCs in sensing, protein activity regulation, cell behavior manipulation, and biomedicine.

Molecular beacon mediated circular strand displacement strategy for constructing a ratiometric electrochemical deoxyribonucleic acid sensor

A novel ratiometric electrochemical sensor for sensitive and selective determination of deoxyribonucleic acid (DNA) had been developed based on signal-on and signal-off strategy. The target DNA hybridized with the loop portion of ferrocene (Fc) labeled hairpin probe immobilized on the gold electrode (GE), the Fc away from the surface of GE and the methylene blue (MB) was attached to an electrode surface by hybridization between hairpin probe and MB labeled primer. Such conformational changes resulted in the oxidation peak current of Fc decreased and that of MB increased, and the changes of dual signals are linear with the concentration of DNA. Furthermore, with the help of strand-displacement polymerization, polymerase catalyzed the extension of the primer and the sequential displacement of the target DNA, which led to the release of target and another polymerization cycle. Thus the circular strand displacement produced the multiplication of the MB confined near the GE surface and Fc got away from the GE surface. Therefore, the recognition of target DNA resulted in both the “signal-off” of Fc and the “signal-on” of MB for dual-signal electrochemical ratiometric readout. The dual signal strategy offered a dramatic enhancement of the stripping response. The dynamic range of the target DNA detection was from 10−13 to 10−8molL−1 with a detection limit down to 28fM level. Compared with the single signaling electrochemical sensor, the dual-signaling electrochemical sensing strategy developed in this paper was more selective. It would have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins.

Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator

XR5944, a deoxyribonucleic acid (DNA) bis-intercalator with potent anticancer activity, can bind the estrogen response element (ERE) sequence to inhibit estrogen receptor-α activities. This novel mechanism of action may be useful for overcoming drug resistance to currently available antiestrogen treatments, all of which target the hormone-receptor complex. Here we report the nuclear magnetic resonance solution structure of the 2:1 complex of XR5944 with the naturally occurring TFF1-ERE, which exhibits important and unexpected features. In both drug–DNA complexes, XR5944 binds strongly at one intercalation site but weakly at the second site. The sites of intercalation within a native promoter sequence appear to be context and sequence dependent. The binding of one drug molecule influences the binding site of the second. Our structures underscore the fact that the DNA binding of a bis-intercalator is directional and different from the simple addition of two single intercalation sites. Our study suggests that improved XR5944 bis-intercalators targeting ERE may be designed through optimization of aminoalkyl linker and intercalation moieties at the weak binding sites.

Sequence-specific DNA labeling using methyltransferases.

Sequence-specific labeling of native deoxyribonucleic acid (DNA) still represents a more-or-less unsolved problem. Difficulties mainly arise from the necessity to combine two different functions: sequence-specific recognition of DNA and covalent bond formation between the label and DNA. DNA methyltransferases (MTases) naturally possess these two functions and transfer a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) to adenine or cytosine residues within specific DNA sequences, typically ranging from two to eight base pairs. Unfortunately, the methyl group itself is a very limited reporter group and it would be desirable to transfer larger chemical entities with DNA MTases. Replacement of the methionine side chain of the natural cofactor AdoMet by an aziridinyl residue leads to the synthetic cofactor N-adenosylaziridine, which is quantitatively, base- and sequence-specifically coupled with DNA in a DNA MTase-catalyzed reaction. By attaching interesting reporter groups to a suitable position of N-adenosylaziridine a large variety of new synthetic cofactors are obtained for sequence-specific labeling of DNA. This method is illustrated by coupling primary amino groups and biotin to short duplex oligodeoxynucleotides or plasmid DNA using the DNA MTase M.TaqI.

Transcriptional repressor CopR: Structure model-based localization of the deoxyribonucleic acid binding motif

The plasmid pIP501 encoded transcriptional repressor CopR is one of the two regulators of plasmid copy number. CopR binds as a dimer to a nearly palindromic operator with the consensus sequence 5'-CGTG. Intermediate sequence searches revealed a significant structural relationship between CopR and the bacteriophage P22 c2 and the 434 c1 repressors. In this report we describe the experimental verification of a CopR homology model, which is based on a fairly low-sequence identity of 13.8% to P22 c2 repressor. A model for the complex of CopR with the deoxyribonucleic acid (DNA) target was built on the basis of experimental footprinting data, the above-mentioned CopR homology model, and the crystal structure of the 434 c1 repressor-DNA complex. Site-directed mutagenesis was used to test the function of amino acids involved in sequence and nonsequence-specific DNA recognition and amino acids important for correct protein folding. CD measurements were performed to detect structural changes caused by the mutations. Exchanges of residues responsible for sequence-specific DNA recognition reduced binding to a nonspecific level. Mutations of amino acids involved in nonspecific DNA binding lead to decreased binding affinity while maintaining selectivity. Substitution of amino acids necessary for proper folding caused dramatic structural changes. The experimental data support the model of CopR as a helix-turn-helix protein belonging to the lambda repressor superfamily.