No abstract

A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of `third generation' instruments that will sequence a diploid mammalian genome for ~$1,000 in ~24 h.

The electrical noise characteristics of ionic current through organic and synthetic nanopores have been investigated. Comparison to proteinaceous alpha-Hemolysin pores reveals two dominant noise sources in silicon nitride nanometre-scale pores: a high-frequency noise associated with the capacitance of the silicon support chip (dielectric noise), and a low-frequency current fluctuation with 1/fα characteristics (flicker noise). We present a technique for reducing the dielectric noise by curing polydimethylsiloxane (PDMS) on the nanopore support chip. This greatly improves the performance of solid-state nanopore devices, yielding an unprecedented signal-to-noise ratio when observing dsDNA translocation events and ssDNA probe capture for force spectroscopy applications.

Figure 4. Comparison of single-mismatch detection with gold-quenched beacons versus DABCYL-quenched beacons. Titration of 5 µM of random target mixed with 4.2 nM of gold-DNA-rhodamine 6G conjugate and 0.6 µM of gold (A), and 5 µM of random target mixed with 10 nM of molecular beacon (B), with the perfect target (target 2) and the mismatch one (target 3). Target concentrations vary from 67 pM to 13 µM. For both probes, the perfect target (solid line) produces a faster and sharper increase of fluorescence than the target containing the mismatch (dashed line). Fluorescence intensities due to the buffer and the gold have been subtracted. The inset graphs in (A) and (B) show the evolution of the fluorescence as a function of time when the probe is mixed with 5 µM of random targets. In both cases, the random targets do not induce any change of fluorescence of the probe during the time of the titration. The hybridization is thus very specific to the matched or the mismatched targets. (C) Ratio between the titration curve with the perfect target (target 2) and the titration curve with the mismatched one (target 3). (D) Resolution of a matched and a mismatched target, competing for hybridization. Molecular beacon (dashed line), gold-DNA-dye conjugate (solid line). α is the population ratio of match to mismatch targets. The concentration of perfect target is fixed at 0.2 µM. D

We have engineered a nanosensor for sequence-specific detection of single nucleic acid molecules across a lipid bilayer. The sensor is composed of a protein channel nanopore (alpha-hemolysin) housing a DNA probe with an avidin anchor at the 5' end and a nucleotide sequence designed to noncovalently bind a specific single-stranded oligonucleotide at the 3' end. The 3' end of the DNA probe is driven to the opposite side of the pore by an applied electric potential, where it can specifically bind to oligonucleotides. Reversal of the applied potential withdraws the probe from the pore, dissociating it from a bound oligonucleotide. The time required for dissociation of the probe-oligonucleotide duplex under this force yields identifying characteristics of the oligonucleotide. We demonstrate transmembrane detection of individual oligonucleotides, discriminate between molecules differing by a single nucleotide, and investigate the relationship between dissociation time and hybridization energy of the probe and analyte molecules. The detection method presented in this article is a candidate for in vivo single-molecule detection and, through parallelization in a synthetic device, for genotyping and global transcription profiling from small samples.

Background: DNA polymerases translocate along DNA by one nucleotide in each catalytic cycle. Results: The DNA polymerase translocation step is observed with single nucleotide and submillisecond precision. Conclusion: DNA polymerase complexes fluctuate between pre-and post-translocation states and are rectified to the posttranslocation state by dNTP. Significance: These results provide insight into the translocation mechanism and its integration into the DNA polymerase catalytic pathway.

Mutational characterisation in multiple myeloma (MM) currently relies on bone marrow (BM) biopsy, which fails to capture the putative spatial and genetic heterogeneity of this multifocal disease. Analysis of plasma (PL)-derived circulating free tumour DNA (ctDNA) as an adjunct to BM biopsy, for mutational characterisation and tracking disease progression, was evaluated. Paired BM MM cell DNA and ctDNA from 33 relapsed/refractory (RR) and 15 newly diagnosed (ND) patients were analysed for KRAS, NRAS, BRAF and TP53 mutations using the OnTarget Mutation Detection (OMD) platform. OMD detected 128 mutations (PL=31, BM=59, both=38) indicating the presence of PL mutations (54%). A higher frequency of PL-only mutations was detected in RR patients than ND (27.2% vs 6.6%, respectively), authenticating the existence of spatial and genetic heterogeneity in advanced disease. Activating RAS mutations were more highly prevalent than previously described with 69% harboring at least one RAS mutation. Sequential ctDNA quantitation with droplet digital PCR through longitudinal PL tracking of specific clones in seven patients demonstrated changes in fractional abundance of certain clones reflective of the disease status. We conclude that ctDNA analysis as an adjunct to BM biopsy represents a noninvasive and holistic strategy for improved mutational characterisation and therapeutic monitoring of MM.

The genome of the flowering plant Arabidopsis thaliana has five chromosomes. Here we report the sequence of the largest, chromosome 1, in two contigs of around 14.2 and 14.6 megabases. The contigs extend from the telomeres to the centromeric borders, regions rich in transposons, retrotransposons and repetitive elements such as the 180-base-pair repeat. The chromosome represents 25% of the genome and contains about 6,850 open reading frames, 236 transfer RNAs (tRNAs) and 12 small nuclear RNAs. There are two clusters of tRNA genes at different places on the chromosome. One consists of 27 tRNA(Pro) genes and the other contains 27 tandem repeats of tRNA(Tyr)-tRNA(Tyr)-tRNA(Ser) genes. Chromosome 1 contains about 300 gene families with clustered duplications. There are also many repeat elements, representing 8% of the sequence.