Preliminary nanopore cheminformatics analysis of aptamer-target binding strength

Thomson, Karen; Amin, Iftekhar; Morales, Eric; Winters‐Hilt, Stephen

doi:10.1186/1471-2105-8-s7-s11

Cited by 20 publications

(22 citation statements)

References 23 publications

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“…Protein pores can be selectively functionalized with various probes that can bind individual target molecules with high selectivity and sensitivity[120–122]. The characteristic binding and distinctive current signatures can reveal the identity and concentration of the target analyte[117,122].…”

Section: Current and Prospective Applicationsmentioning

confidence: 99%

Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA

et al. 2013

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Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed.

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Section: Current and Prospective Applicationsmentioning

confidence: 99%

Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA

et al. 2013

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“…Preliminary work with NTD-based detection on short DNA annealing suggests a possible means to examine the miRNA/RISC binding to target 3'UTR region with or without the RISC complexes argonaute proteins intact, where results are expected to improve even more upon refinement using locked nucleic acid transducer/reporter probes (see Discussion). NTD based detection of DNA annealing has been demonstrated on DNA sequences as short as 5 bases [8], and in the presence of a variety of interference agents and chaotropes [3]. NTD based detection has also been demonstrated in a variety of buffer conditions so could be established in a buffer conducive to the RISC complex remaining intact and where the annealing to 3'UTR complement sequence occurs with the binding strength found in vivo.…”

Section: Validation Of Mirna's and Mirna Binding Sites Using A Nanopomentioning

confidence: 99%

“…Five-base annealing using a pseudo-aptamer NTD transducer. Reprinted with permission[8]. Left: The preliminary aptamer experiments are based on the DNA molecule obtained from annealing ssDNA1: 5'-CAAGCTTGGTTTCGATAGGTA-3' with ssDNA2: 5'-ATCGTTTCCAAGCTTG-3'.…”

mentioning

confidence: 99%

Biological system analysis using a nanopore transduction detector: from miRNA validation, to viral monitoring, to gene circuit feedback studies

Winters‐Hilt¹

2017

asms

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The system biologist is currently lacking a general-use method for a gene circuit 'voltmeter' or gene system algorithm 'print statement'. What is needed is a non-destructive, carrier non-modifying, means of testing 'live' biological systems at the single-molecule level. A method using the nanopore transduction detector (NTD) is demonstrated for single-molecule characterization in some situations, so may provide what is lacking. An important aspect of this approach is that use can be made of inexpensive antibody, protein, aptamer, duplex nucleic acid, or nucleic acid annealing molecules (for miRNA and viral monitoring) that have specific binding to the system component of interest. The NTD transducer's specific binding can also be designed to have low affinity binding as needed, such that there can be a 'catch and release' on low copy-number molecular components, such that there is not a disruption to the molecular system under study. NTD transducers are typically constructed by linking a binding moiety of interest to a 14 Stephen Winters-Hilt nanopore current modulator, where the modulator is designed to be electrophoretically drawn to the channel and partly captured, with its captured end distinctively modulating the flow of ions through the channel. Using inexpensive (commoditized) biomolecular components, such as DNA hairpins, this allows for an easily constructed, versatile, platform for biosensing. High specificity high affinity binding also allows a very versatile platform for assaying at the single molecule level, even down to the single isoform level, including molecular substructure profiling, such as glycosylation profiling in antibodies. An inexpensive commoditized pathway for constructing nanopore transducers is demonstrated. Nanopore transduction detector based reporter/event-transducer molecules may serve as a means to perform multicomponent mRNA-miRNA-protein and protein-protein systems analysis in general settings.

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“…These methods provide biologists and chemists a way to get better understanding of the kinetic properties of molecules of interest. By using a nanopore detector, two bifunctional aptamers could be examined [55]. The nanopore detector is biologically based and uses a protein, [58] the α-hemolysin (α-HL) toxin produced by the bacterium Staphylococcus aureus, to create a pore through a phospholipid bilayer by self-assembly.…”

Section: Different Materials Structures Used In Biosensormentioning

confidence: 99%

Advances of Nanotechnology Applied to Biosensors

Chen¹,

Dai²,

Cui³

2011

Nano BioMed ENG

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Up to date, application of nanomaterials and nanotechnology has made great advances. Many novel nanomaterials with unique properties are increasingly being exploited to apply for biosensors, improving the property of biosensor and making them higher selectivity and sensitivity, less response time and lower detective limitation. Here we review some of the main advances in this field over the past few years, explore the application prospects, and discuss the issues, approaches, and challenges, with the amin of promting to develop nanomaterials-based biosensor nanotechnology and improving their application in disease diagnosis and biosafety examination.

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Preliminary nanopore cheminformatics analysis of aptamer-target binding strength

Cited by 20 publications

References 23 publications

Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA

Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA

Biological system analysis using a nanopore transduction detector: from miRNA validation, to viral monitoring, to gene circuit feedback studies

Advances of Nanotechnology Applied to Biosensors

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