Single nucleotide polymorphism (SNP) discriminations by nanopore sensing

Single Nucleotide Polymorphisms (SNPs) are a common type of nucleotide alterations across the genome. A rapid but accurate detection of individual or SNP panels can lead to the right and in-time treatments which possibly save lives. In one of our studies, nanopore is introduced to rapidly detect BRAF 1799 T-A mutation (V600E), with the help of an Ap-dA cross-link right at the mutation site. These sequence-specific crosslinks are formed upon strong covalent interactions between probe based abasic sites (Ap) and target based deoxy-adenosine (dA) residues. Duplexes stabilized by the crosslink complexes create indefinite blocking signatures when captured in the nanopore, creating a high contrast compared to the "spike-like" translocations events produced by the un-crosslinked and wildtype duplexes. Those consistent blocking events couldn't be resolved unless an inverted voltage is applied. In a 1:1 BRAF mutant-wildtype mixture, the nanopore can successfully discriminate between the two sequences in a quantitative manner. In summary, nanopore paired with sequence-specific crosslink can detect a specific type of SNP with a high contrast manner. In another study, nanopore sensing is modified to be capable of detections with multiple SNPs in a single detection mix. To achieve this, an RNA homopolymer barcode is integrated into the probe sequence so nanopore can read out a distinctive level signature when the target-probe duplex is de-hybridizing through the pore. Since different RNA homopolymers (e.g. Poly rA and Poly rC) can generate signature levels distinctive from each other and other DNA sequences, they can be applied to generate characteristic patterns that simultaneously highlight multiple SNPs in the mixture. In this study, we assigned two different RNA barcodes (Poly rA and Poly rC) to label KRAS G12D and Tp53 R172H SNPs (both T[right arrow]A mutations) in the solution. During nanopore readout, the KRAS G12D containing duplex generates a "downward" step pattern but Tp53 R172H always has an "upward" step pattern, the high contrast between those two patterns makes recognition easy enough with naked eyes, and further statistical analysis is unnecessary. Theoretically, at least four different barcodes can be implemented at the same time, furthermore, the length of the barcode can also affect the barcode pattern. Thus, in theory, a panel of more than 10 SNPs can be identified simultaneously.Includes bibliographical reference

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing <i>Escherichia coli</i> (STEC) serotype O157:H7, and cancer-derived <i>EGFR</i> L858R and <i>KRAS</i> G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing <i>Escherichia coli</i> (STEC) serotype O157:H7, and cancer-derived <i>EGFR</i> L858R and <i>KRAS</i> G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing <i>Escherichia coli</i> (STEC) serotype O157:H7, and cancer-derived <i>EGFR</i> L858R and <i>KRAS</i> G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations

Real-time detection of dopamine -- aptamer interactions in a nanopore: a label-free toolkit for study of nucleic-acid-based molecular sensors.

Understanding how small molecules regulate nucleic acid structures is important in both biomechanism elucidation and biotechnological applications. Through the conformational variation, native nucleic acid motifs can be used as the targets to screen therapeutic compounds; In vitro selected aptamers can be used to detect small molecule biomarkers such as neurotransmitters and hormones, and ligand-triggered riboswitches can be designed to control gene expressions. All these applications need a rapid universal platform to detect nucleic acid conformational change in response to small molecule binding. Here we propose a label-free, non-invasive, and modular aptamer-inlaid nanopore capable of revealing time-resolved single nucleic acid molecule conformational transitions at the millisecond resolution. When a dopamine aptamer is docked in the MspA protein pore, the ion current through the pore can characteristically vary as the aptamer transitions between different conformations, recording a sequence of current fingerprints for binding and release of single neurotransmitter molecules from the aptamer. Without the need to mix the aptamer and the ligand, the sensor can quantify the target neurotransmitter, discriminate between different neurotransmitters, assay nucleic acid-ligand interactions, elucidate the ligand selectivity mechanism and pinpoint the ligand docking motifs in the aptamer, offering a potential nanopore toolbox for multiple small molecule biomarkers detection and screening nucleic acid-targeted small molecule regulators. Finally, we optimize the sensitivity of the nanopore sensor by employing divalent ions.Includes bibliographical references