The NTD Nanoscope: potential applications and implementations
<p>Abstract</p> <p>Background</p> <p>Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequencing; (iii) protein is...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-10-01
|
| Series: | BMC Bioinformatics |
| _version_ | 1828301255333642240 |
|---|---|
| author | Horton-Chao Evenie Winters-Hilt Stephen Morales Eric |
| author_facet | Horton-Chao Evenie Winters-Hilt Stephen Morales Eric |
| author_sort | Horton-Chao Evenie |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequencing; (iii) protein isoform assaying; and (iv) biosensing via antibody or aptamer coupled molecules. Nanopore event transduction involves single-molecule biophysics, engineered information flows, and nanopore cheminformatics. The NTD Nanoscope has seen limited use in the scientific community, however, due to lack of information about potential applications, and lack of availability for the device itself. Meta Logos Inc. is developing both pre-packaged device platforms and component-level (unassembled) kit platforms (the latter described here). In both cases a lipid bi-layer workstation is first established, then augmentations and operational protocols are provided to have a nanopore transduction detector. In this paper we provide an overview of the NTD Nanoscope applications and implementations. The NTD Nanoscope Kit, in particular, is a component-level reproduction of the standard NTD device used in previous research papers.</p> <p>Results</p> <p>The NTD Nanoscope method is shown to functionalize a single nanopore with a channel current modulator that is designed to transduce events, such as binding to a specific target. To expedite set-up in new lab settings, the calibration and troubleshooting for the NTD Nanoscope kit components and signal processing software, the NTD Nanoscope Kit, is designed to include a set of test buffers and control molecules based on experiments described in previous NTD papers (the model systems briefly described in what follows). The description of the Server-interfacing for advanced signal processing support is also briefly mentioned.</p> <p>Conclusions</p> <p>SNP assaying, SNP discovery, DNA sequencing and RNA-seq methods are typically limited by the accuracy of the error rate of the enzymes involved, such as methods involving the polymerase chain reaction (PCR) enzyme. The NTD Nanoscope offers a means to obtain higher accuracy as it is a single-molecule method that does not inherently involve use of enzymes, using a functionalized nanopore instead.</p> |
| first_indexed | 2024-04-13T13:20:52Z |
| format | Article |
| id | doaj.art-99c84a035bc7488981deccd5c10c983f |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T13:20:52Z |
| publishDate | 2011-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-99c84a035bc7488981deccd5c10c983f2022-12-22T02:45:19ZengBMCBMC Bioinformatics1471-21052011-10-0112Suppl 10S2110.1186/1471-2105-12-S10-S21The NTD Nanoscope: potential applications and implementationsHorton-Chao EvenieWinters-Hilt StephenMorales Eric<p>Abstract</p> <p>Background</p> <p>Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequencing; (iii) protein isoform assaying; and (iv) biosensing via antibody or aptamer coupled molecules. Nanopore event transduction involves single-molecule biophysics, engineered information flows, and nanopore cheminformatics. The NTD Nanoscope has seen limited use in the scientific community, however, due to lack of information about potential applications, and lack of availability for the device itself. Meta Logos Inc. is developing both pre-packaged device platforms and component-level (unassembled) kit platforms (the latter described here). In both cases a lipid bi-layer workstation is first established, then augmentations and operational protocols are provided to have a nanopore transduction detector. In this paper we provide an overview of the NTD Nanoscope applications and implementations. The NTD Nanoscope Kit, in particular, is a component-level reproduction of the standard NTD device used in previous research papers.</p> <p>Results</p> <p>The NTD Nanoscope method is shown to functionalize a single nanopore with a channel current modulator that is designed to transduce events, such as binding to a specific target. To expedite set-up in new lab settings, the calibration and troubleshooting for the NTD Nanoscope kit components and signal processing software, the NTD Nanoscope Kit, is designed to include a set of test buffers and control molecules based on experiments described in previous NTD papers (the model systems briefly described in what follows). The description of the Server-interfacing for advanced signal processing support is also briefly mentioned.</p> <p>Conclusions</p> <p>SNP assaying, SNP discovery, DNA sequencing and RNA-seq methods are typically limited by the accuracy of the error rate of the enzymes involved, such as methods involving the polymerase chain reaction (PCR) enzyme. The NTD Nanoscope offers a means to obtain higher accuracy as it is a single-molecule method that does not inherently involve use of enzymes, using a functionalized nanopore instead.</p> |
| spellingShingle | Horton-Chao Evenie Winters-Hilt Stephen Morales Eric The NTD Nanoscope: potential applications and implementations BMC Bioinformatics |
| title | The NTD Nanoscope: potential applications and implementations |
| title_full | The NTD Nanoscope: potential applications and implementations |
| title_fullStr | The NTD Nanoscope: potential applications and implementations |
| title_full_unstemmed | The NTD Nanoscope: potential applications and implementations |
| title_short | The NTD Nanoscope: potential applications and implementations |
| title_sort | ntd nanoscope potential applications and implementations |
| work_keys_str_mv | AT hortonchaoevenie thentdnanoscopepotentialapplicationsandimplementations AT wintershiltstephen thentdnanoscopepotentialapplicationsandimplementations AT moraleseric thentdnanoscopepotentialapplicationsandimplementations AT hortonchaoevenie ntdnanoscopepotentialapplicationsandimplementations AT wintershiltstephen ntdnanoscopepotentialapplicationsandimplementations AT moraleseric ntdnanoscopepotentialapplicationsandimplementations |