Nanopore Decoding of Oligonucleotides in DNA Computing

Abstract

In conventional DNA-computation methods involving logic gate operations, the output molecules are detected and decoded mainly by gel electrophoresis or fluorescence measurements. To employ rapid and label-free decoding, nanopore technology, an emerging methodology for single-molecule detection or DNA sequencing, is proposed as a candidate for electrical and simple decoding of DNA computations. This review describes recent approaches to decoding DNA computation using label-free and electrical nanopore measurements. Several attempts have been successful in DNA decoding with the nanopore either through enzymatic reactions or in water-in-oil droplets. Additionally, DNA computing combined with nanopore decoding has clinical applications, including microRNA detection for early diagnosis of cancers. Because this decoding methodology is still in development and not yet widely accepted, this review aims to inform the scientific community regarding usefulness.

Recognition of Single‐Point Mutation Using a Biological Nanopore

“…Nanopore technology [12][13][14][15][16] is a promi sing candidate for the rapid detection of mutated ctDNAs. There are two different nanopore approaches for liquid biopsy: nanopore sequencing of ctDNA or direct sensing of ctDNA using a 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.…”

Recent Advances in Origins of Life Research by Biophysicists in Japan

“…Coupling these imaging and sequencing advances with novel microfluidics and nanotechnology would be the next important avenue to consider for OoL researchers. Further development of nanopore technology (used in the single molecule sequencing methods described above [152]) [169,170] would further allow analysis of a wider range of prebiological polymer systems, while additionally opening up the possibility of the incorporation of sequencing technologies onto in situ life detection missions [171]. While microfluidics technologies have already been incorporated into sequencing technologies [172], recent advances in coupling microfluidic systems with compartment formation and manipulation have been developed by Masahiro Takinoue's lab at Tokyo Institute of Technology [173] and Hiroyuki Noji's lab at University of Tokyo [174,175].…”

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.…”