Showing papers by "Jens H. Gundlach published in 2014"

Decoding long nanopore sequencing reads of natural DNA

Abstract: Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length, which can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. This work provides a foundation for nanopore sequencing of long, natural DNA strands.

A high-precision mechanical absolute-rotation sensor.

Abstract: We have developed a mechanical absolute-rotation sensor capable of resolving ground rotation angle of less than 1 nrad / Hz above 30 mHz and 0.2 nrad / Hz above 100 mHz about a single horizontal axis. The device consists of a meter-scale beam balance, suspended by a pair of flexures, with a resonance frequency of 10.8 mHz. The center of mass is located 3 μm above the pivot, giving an excellent horizontal displacement rejection of better than 3 × 10−5 rad/m. The angle of the beam is read out optically using a high-sensitivity autocollimator. We have also built a tiltmeter with better than 1 nrad / Hz sensitivity above 30 mHz. Co-located measurements using the two instruments allowed us to distinguish between background rotation signal at low frequencies and intrinsic instrument noise. The rotation sensor is useful for rotational seismology and for rejecting background rotation signal from seismometers in experiments demanding high levels of seismic isolation, such as Advanced Laser Interferometer Gravitational-wave Observatory.

A high-precision mechanical absolute-rotation sensor

Abstract: We have developed a mechanical absolute-rotation sensor capable of resolving ground rotation angle of less than 1 nrad$/\sqrt{\text{Hz}}$ above $30$ mHz and 0.2 nrad$/\sqrt{\text{Hz}}$ above $100$ mHz about a single horizontal axis. The device consists of a meter-scale beam balance, suspended by a pair of flexures, with a resonance frequency of 10.8 mHz. The center of mass is located 3 $\mu$m above the pivot, giving an excellent horizontal displacement rejection of better than $3\times10^{-5}$ rad/m. The angle of the beam is read out optically using a high-sensitivity autocollimator. We have also built a tiltmeter with better than 1 nrad$/\sqrt{\text{Hz}}$ sensitivity above 30 mHz. Co-located measurements using the two instruments allowed us to distinguish between background rotation signal at low frequencies and intrinsic instrument noise. The rotation sensor is useful for rotational seismology and for rejecting background rotation signal from seismometers in experiments demanding high levels of seismic isolation, such as Advanced LIGO.

Compositions and methods for polynucleotide sequencing

Abstract: Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.

Selective modification of polymer subunits to improve nanopore-based analysis

Abstract: The present disclosure provides method and systems for improving nanopore-based analyses of polymers. The disclosure provides methods for selectively modifying one or more monomeric subunit(s) of a kind a pre-analyte polymer that results polymer analyte with a modified subunit. The polymer analyte produces a detectable signal in a nanopore-based system. The detectable signal, and/or its deviation from a reference signal, indicates the location of the modified subunit in the polymer analyte and, thus, permits the identification of the subunit at that location in the original pre- analyte polymer.

Interferometric quasi-autocollimator

Abstract: Systems and method are disclosed for measuring small angular deflections of a target using weak value amplification. A system includes a beam source, a beam splitter, a target reflecting surface, a photodetector, and a processor. The beam source generates an input beam that is split into first and second beams by the beam splitter. The first and second beams are propagated to the target reflecting surface, at least partially superimposed at the target reflecting surface, and incident to the target reflecting surface normal to the target reflecting surface. The first beam is reflected an additional even number of times during propagation to the photodetector. The second beam is reflected an additional odd number of times during propagation to the photodetector. The first and second beams interfere at the photodetector so as to produce interference patterns. The interference patterns are interpreted to measure angular deflections of the target reflecting surface.

Nanopore Sequencing of the phi X 174 genome

Abstract: Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost, and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length that can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. All methods and data are made fully available.

Nanopore-based analysis of protein characteristics

Abstract: Methods for nanopore-based protein analysis are provided. The methods address the characterization of a target protein analyte, which has a dimension greater than an internal diameter of the nanopore tunnel, and which is also physically associated with a polymer. The methods further comprise applying an electrical potential to the nanopore system to cause the polymer to interact with the nanopore tunnel. The ion current through the nanopore is measured to provide a current pattern reflective of the structure of the portion of the polymer interacting with the nanopore tunnel. This is used as a metric for characterizing the associated protein that does not pass through the nanopore.