Use of Electrocatalysis for Differentiating DNA Polymorphisms and Enhancing the Sensitivity of Electrochemical Nucleic Acid-Based Sensors with Covalent Redox Tags-Part II

Single-nucleotide polymorphisms (SNPs), insertion/deletion (indel) polymorphisms, and DNA methylation are the most frequent types of genetic variations. As such, DNA polymorphisms play significant roles in genetic mapping and diagnostics. Thus, analytical methods enabling DNA polymorphism detection will provide an invaluable means for early disease diagnosis. However, no single electrochemical nucleic acid-based sensor has achieved the detection of the three major polymorphisms (SNPs, indel polymorphisms, and DNA methylation) with sufficient specificity and sensitivity. In response, we explore the utilization of a catalytic reaction between methylene blue (MB) covalently linked to surface-bound nucleic acid and freely diffusing ferricyanide (Fe(CN)₆^3-) to improve specificity and sensitivity of DNA polymorphism detection. We find that the dynamics of the nucleic acid tether is an additional rate-limiting factor for the electrocatalytic reaction, in addition to the more traditional kinetic and excess factors. Our proof-of-concept experiments demonstrate that the use of electrocatalysis enables differentiation of the three polymorphisms when target sequences are present at 10 nM. We hypothesize that this ability is a result of the distinct dynamics of the DNA probe with each respective polymorphism. In addition to the specificity the sensor displays, the sensor achieves a 20 pM limit of detection. We believe that the electrocatalysis between nucleic acid-tethered MB and Fe(CN)₆^3- is highly promising for electrochemical nucleic acid-based sensors to achieve better specificity and sensitivity.

An efficient DNA-fueled molecular machine for the discrimination of single-base changes

A new strategy for single-base polymorphism (SNP) detection based on the assembly of DNA-AuNPs (gold nanoparticles) driven by a DNA-fueled molecular machine, is established and optimized. It is highly efficient, works at room temperature, and is easy to handle. A single-base change on an oligonucleotide strand is unambiguously discriminated for either SNPs or insertions and deletions (indels). The strategy is demonstrated to detect a mutation in the breast cancer gene BRCA1 in homogeneous solution at room temperature.

Accurate zygote-specific discrimination of single-nucleotide polymorphisms using microfluidic electrochemical DNA melting curves

We report the first electrochemical system for the detection of single-nucleotide polymorphisms (SNPs) that can accurately discriminate homozygous and heterozygous genotypes using microfluidics technology. To achieve this, our system performs real-time melting-curve analysis of surface-immobilized hybridization probes. As an example, we used our sensor to analyze two SNPs in the apolipoprotein E (ApoE) gene, where homozygous and heterozygous mutations greatly affect the risk of late-onset Alzheimer's disease. Using probes specific for each SNP, we simultaneously acquired melting curves for probe-target duplexes at two different loci and thereby accurately distinguish all six possible ApoE allele combinations. Since the design of our device and probes can be readily adapted for targeting other loci, we believe that our method offers a modular platform for the diagnosis of SNP-based diseases and personalized medicine.

Detection of single-nucleotide variations by monitoring the blinking of fluorescence induced by charge transfer in DNA

Charge transfer dynamics in DNA: Photo-induced charge separation and charge-recombination dynamics in DNA was assessed by monitoring the blinking of fluorescence. Single nucleotide variations, mismatch and one base deletion, were differentiated based on the length of the off-time of the blinking, which corresponds to the lifetime of the charge-separated state.