Determination of the binding site size of hexaammineruthenium(iii) inside monolayers of DNA on gold

Hexaammineruthenium(iii), RuHex³⁺, is a DNA-binding metal complex that is widely used as a redox marker for the indirect determination of DNA coverage at the electrode surface. The conversion of electrochemically quantifiable surface excess of RuHex³⁺ into DNA surface coverage requires the knowledge of the binding site size of RuHex³⁺ (s). Traditionally, s on surface-immobilized DNA has been assumed to be equivalent to that on solution-phase DNA, which was experimentally determined in previous studies. Nevertheless, the different local microenvironments existing inside DNA monolayers in comparison to that in bulk solutions cast doubt on the validity of this assumption. In this report, we used electrochemical techniques to investigate s on surface-immobilized DNA. The values of s inside the DNA monolayers were found to be significantly smaller than that reported on solution-phase DNA. Besides, s was found to depend on the DNA packing density and became larger by increasing the DNA surface coverage or hybridizing the surface-tethered DNAs with complementary strands. Our data indicate that the RuHex³⁺ method, in which an s value of 3 nucleotides is used for the conversion of RuHex³⁺ to DNA surface coverage, does not always give reliable results.

Targeted Detection of Single-Nucleotide Variations: Progress and Promise

Advances in nucleic acid sequencing and genotyping technologies have facilitated the discovery of an increasing number of single-nucleotide variations (SNVs) associated with disease onset, progression, and response to therapy. The reliable detection of such disease-specific SNVs can ensure timely and effective therapeutic action, enabling precision medicine. This has driven extensive efforts in recent years to develop novel methods for the fast and cost-effective analysis of targeted SNVs. In this Review, we highlight the most recent and significant advances made toward the development of such methodologies.

Electrochemical switching with 3D DNA tetrahedral nanostructures self-assembled at gold electrodes

Nanomechanical switching of functional three-dimensional (3D) DNA nanostructures is crucial for nanobiotechnological applications such as nanorobotics or self-regulating sensor and actuator devices. Here, DNA tetrahedral nanostructures self-assembled onto gold electrodes were shown to undergo the electronically addressable nanoswitching due to their mechanical reconfiguration upon external chemical stimuli. That enables construction of robust surface-tethered electronic nanodevices based on 3D DNA tetrahedra. One edge of the tetrahedron contained a partially self-complementary region with a stem-loop hairpin structure, reconfigurable upon hybridization to a complementary DNA (stimulus DNA) sequence. A non-intercalative ferrocene (Fc) redox label was attached to the reconfigurable tetrahedron edge in such a way that reconfiguration of this edge changed the distance between the electrode and Fc.

Electroanalysis of single-nucleotide polymorphism by hairpin DNA architectures

Genetic analysis of infectious and genetic diseases and cancer diagnostics require the development of efficient tools for fast and reliable analysis of single-nucleotide polymorphism (SNP) in targeted DNA and RNA sequences often responsible for signalling disease onset. Here, we highlight the main trends in the development of electrochemical genosensors for sensitive and selective detection of SNP that are based on hairpin DNA architectures exhibiting better SNP recognition properties compared with linear DNA probes. SNP detection by electrochemical hairpin DNA beacons is discussed, and comparative analysis of the existing SNP sensing strategies based on enzymatic and nanoparticle signal amplification schemes is presented.