DNA Logic Operation with Nanopore Decoding To Recognize MicroRNA Patterns in Small Cell Lung Cancer

Abstract

Although DNA computation has traditionally been developed for parallel calculations in molecular analyses, this approach has recently been considered for use in diagnostic or medical applications in living systems. In this study, we propose that the DNA logic operation may be a powerful tool for the recognition of microRNA patterns, which may have applications for the early diagnosis of cancers. We developed a rapid, label-free decoding method for output diagnostic molecules using nanopore measurements. We designed diagnostic DNAs that autonomously recognized two microRNAs, miR-20a and miR-17-5p, and formed a four-way junction structure that was captured in the nanopore, showing long blocking currents. We analyzed the blocking duration based on the central limit theorem and found that four different operations, i.e., (0, 0), (0, 1), (1, 0), and (1, 1), could be discriminated. This pattern recognition method has been differentiated from simple detection methods based on DNA computing and nanopore technologies.

Recognition of Single‐Point Mutation Using a Biological Nanopore

“…We have previously developed single molecular detection methods using nanopores, [24][25][26][27][28][29][30][31] including analysis of the unzip ping time of doublestranded DNA and RNA with bootstrap ping. [14,29] Hiratani and Kawano applied nanopore decoding of DNA computing outputs for miRNA pattern recognition. [29] Two miRNAs that are overexpressed and secreted from tumor cells were recognized via diagnostic DNA (dgDNA) hybridiza tion, with formation of a fourway junction in the presence of both miRNAs.…”

“…[32][33][34] In this study, discernment of the position of the singlepoint mutation in oligonucleotides was achieved by analysis of unzip ping behavior in a method analogous to that of Hiratani's work. [29] The target oligonucleotides (21 nt) based on an EGFR sequence were hybridized with probe DNA to form a doublestranded Here the recognition of a single-point mutation in oligonucleotides is described by using nanopore measurements. The translocation behavior of a series of mutated DNA strands, hybridized with a complementary DNA probe, is analyzed via blocking current and unzipping time.…”

Nanopore Decoding of Oligonucleotides in DNA Computing

“…Although this method achieved accurate detection of four different miRNAs, it was difficult to measure the amounts of respective miRNAs, because differences in the blocking levels were too close to allow discrimination. Very recently, the analysis of the duration of the blocking instead of the blocking current are proposed for the pattern recognition of miRNA expression using AND logic gate with nanopore technology …”

“…Very recently, the analysis of the duration of the blocking instead of the blocking current are proposed for the pattern recognition of miRNA expression using AND logic gate with nanopore technology. [67] Another advantage of using nanopore technology for miRNA detection is its sensitivity. In conventional analytic methods, such as microscopic or electrochemical methods, sensitivity relies upon signal intensity.…”

De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

“…As a result of great research efforts, the nanopore sequencer has been commercialized as an inexpensive and portable DNA sequencer device. Besides DNA sequencing, a wide variety of nanopore studies have been proposed, such as small molecule detection using an adapter 25 or DNA aptamer, 26 nanopore mass spectroscopy, 27 decoding of DNA computations, [28][29][30][31][32] and protein or peptide detection. [33][34][35] The choice of applicable target molecule is sometimes limited because the selectivity of nanopore sensing depends on the pore size, and the size variation of natural pore-forming proteins is insufficient for the detection of a range of molecules.…”