Featured
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Method to Watch |
Nanopores for sequencing proteins
Developments in nanopore-based peptide detection and sequencing show promise of a breakthrough.
- Arunima Singh
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Article |
Peptide sequencing based on host–guest interaction-assisted nanopore sensing
A phenylalanine-containing peptide probe can be used for discriminating all 20 amino acids via current blockage during translocation through an α-hemolysin (αHL) nanopore. The paper provides proof-of-concept peptide sequencing demonstrations.
- Yun Zhang
- , Yakun Yi
- & Hai-Chen Wu
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Article |
Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by nanopore
A Ni2+-modified MspA nanopore construct can unambiguously discriminate the 20 proteogenic amino acids as well as several post-translational modifications.
- Kefan Wang
- , Shanyu Zhang
- & Shuo Huang
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Editorial |
Single-cell proteomics: challenges and prospects
Single-cell proteomics is a challenging goal and an area of rapid methods development. This Focus issue highlights the many paths toward high-throughput, high-sensitivity measurements.
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Comment |
Advances in nanopore direct RNA sequencing
Nanopore direct RNA sequencing (DRS) reads continuous native RNA strands. Early adopters have used this technology to document nucleotide modifications and 3′ polyadenosine tails on RNA strands without added chemistry steps. Individual strands ranging in length from 70 to 26,000 nucleotides have been sequenced. In our opinion, broader acceptance of nanopore DRS by molecular biologists and cell biologists will be accelerated by higher basecall accuracy and lower RNA input requirements.
- Miten Jain
- , Robin Abu-Shumays
- & Mark Akeson
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Research Highlight |
Nanopores distinguish RNA modifications
Different nucleotides and derivatives can be read out by MspA-PBA, an engineered nanopore.
- Lin Tang
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Research Highlight |
Reading proteins with nanopores
Two studies use nanopores for single-protein fingerprinting and make headway toward single-protein sequencing.
- Rita Strack
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Research Highlight |
Nanopore-detectable reporter proteins
NanoporeTERs, engineered reporter proteins, can be detected on MinION nanopore sensor arrays.
- Arunima Singh
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Research Highlight |
A dual-constriction biological nanopore
Addition of a second constriction to CsgG-family nanopores improves the accuracy of homopolymer sequencing.
- Arunima Singh
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Research Highlight |
Touch-and-go sensing
A protein nanopore sensor detects transient protein–protein interactions at single-molecule resolution.
- Karin Kuehnel
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Tools in Brief |
Genome scaffolding while you sequence
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Brief Communication |
Mapping DNA methylation with high-throughput nanopore sequencing
A tool based on hidden Markov model and hierarchical Dirichlet process (HMM-HDP) can call two methylated cytosine variants and a methylated adenine variant directly from genomic DNA using nanopore sequencing data.
- Arthur C Rand
- , Miten Jain
- & Benedict Paten
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Brief Communication |
Detecting DNA cytosine methylation using nanopore sequencing
A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human genomic DNA without chemical treatment.
- Jared T Simpson
- , Rachael E Workman
- & Winston Timp
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Tools in Brief |
Nanopore-based protein fingerprinting
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Research Highlights |
Teaching nanopores to speak protein
A proof-of-concept platform demonstrates the feasibility of nanopore-based sequencing of polypeptide chains.
- Michael Eisenstein
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Tools in Brief |
Mapping nanopore sequence reads
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Methods in Brief |
Nanopores for multiplexed protein sensing
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Research Highlights |
Nanopores and the helicase two-step
A nanopore used for sequencing gives a detailed view of how motor proteins behave on DNA.
- Tal Nawy
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Technology Feature |
Nanopores: a sequencer in your backpack
It's been a long wait for nanopore sequencing technology. Over 1,000 labs are testing the first commercial device and publishing results. Researchers tell Nature Methods about their experiences putting these early instruments through their paces. And more technology is in the works.
- Vivien Marx
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Brief Communication |
A complete bacterial genome assembled de novo using only nanopore sequencing data
By error-correcting long nanopore reads and calling a consensus sequence using nanopore signal data, an entire bacterial genome is assembled de novo.
- Nicholas J Loman
- , Joshua Quick
- & Jared T Simpson
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Article |
Improved data analysis for the MinION nanopore sequencer
Improved error assessment and read alignment on the MinION nanopore sequencing platform allow for calling of single-nucleotide variants and resolving the repeat structure of an assembly gap in the human X chromosome.
- Miten Jain
- , Ian T Fiddes
- & Mark Akeson
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Tools in Brief |
Nanopore sequencing for bacterial trouble spots
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Method to Watch |
Nanopores for proteins
Nanopores hold promise for single-protein characterization.
- Tal Nawy
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Research Highlights |
It's porin' CNTs
Lipid-coated carbon nanotubes can insert themselves spontaneously into lipid bilayers and live-cell membranes.
- Irene Jarchum
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Research Highlights |
Nanopores read long genomic DNA
An ion-current map characteristic of four nucleotides traversing a protein nanopore allows resequencing of long DNA reads.
- Nicole Rusk
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Research Highlights |
Nanopores sense protein modifications
Protein nanopores can detect post-translational modifications in proteins.
- Tal Nawy
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Methods in Brief |
Nanopore-based protein sequencing
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Method to Watch |
Disruptive nanopores
2013 will see the first commercial nanopore sequencers.
- Nicole Rusk
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Research Highlights |
Changing the channel
Self-assembling DNA nanopores could offer a powerful, customizable tool for a host of biological applications.
- Michael Eisenstein
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News & Views |
Close encounters: integrating nanopores and CMOS amplifiers for single-molecule detection
Using semiconductor processing to construct integrated circuits that reside close to nanopores, researchers demonstrate high-bandwidth, low-noise measurements of DNA translocation through solid-state nanopores.
- John S Oliver
- & Valentin Dimitrov
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Research Highlights |
A nanopore workhorse
Voltage-driven and enzyme-regulated control allows precise ratcheting of a DNA strand in and out of a nanopore.
- Nicole Rusk
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Article |
Integrated nanopore sensing platform with sub-microsecond temporal resolution
The temporal resolution of current signals from solid-state nanopores is improved by integrating a complementary metal-oxide-semiconductor preamplifier with the nanopores in thin silicon nitride membranes.
- Jacob K Rosenstein
- , Meni Wanunu
- & Kenneth L Shepard
Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore
Nanopore-based detection of phosphorylation