Mismatch-guided DNA competitive converter enables expanded detection window for discriminating single nucleotide polymorphisms

Abstract

The subtle free energy differences resulting from single nucleotide mutations pose a challenge for the specificity of nearly all DNA hybridization probes in identifying single nucleotide polymorphisms (SNPs). The narrow detection window between mutant target (MT) and wild-type target (WT) concentrations that produce the same level of detection signals limits the widespread application of current SNP detection technologies. In this paper, we introduce an efficient method for converting single-base information using a rationally designed ratio-signal DNA competitive converter (RDCC). This converter significantly expands the detection window for single-base mutations in nucleic acid sequences by enabling a user-defined conversion of quantitative relationships between detection signals and target concentrations. Both computer simulations and experimental validations have confirmed the effectiveness of RDCC in converting single-base information and expanding the detection window. By balancing both MT and WT signals, RDCC excels in identifying heterozygous samples with low mutation abundances. Additionally, RDCC has been proven to be harmoniously compatible with commonly used nucleic acid amplification techniques, such as PCR. Furthermore, we have demonstrated the practical application value of RDCC through genotyping tests on genomic samples from soybean leaves. Therefore, this study not only develops a powerful tool for SNP detection but also provides a paradigm for the design of specific nucleic acid probes.