Processing of nucleotide sequences

Patent metadata

Field	Value
Publication number	US-2015369772-A1
Application number	US-201414764601-A
Country	US
Kind code	A1
Filing date	Jan 23, 2014
Priority date	Feb 7, 2013
Publication date	Dec 24, 2015
Grant date	—

Abstract

The invention relates to a method and an apparatus ( 100 ) for the processing of nucleotide sequences. An apparatus ( 100 ) according to an embodiment of the invention comprises an array of electrodes ( 120 a, 120 b , . . . ), wherein at least one nanoball (NB) comprising replications of a nucleotide sequence ( 1,2 ) of interest is attached to an electrode to which only one nanoball (NB) of that size can be attached at the same time. Thus a unique association of electrodes ( 120 a, 120 b , . . . ) to nucleotide sequences ( 1,2 ) of interest can be achieved. The nanoballs (NB) are preferably produced by rolling circle amplification. Application of attractive and/or repulsive electric potentials to the electrodes ( 120 a, 120 b , . . . ) can be used to control the attachment of nanoballs (NB). The measurement of changes in the capacitance of electrodes ( 120 a, 120 b , . . . ) can be used to detect and monitor the incorporation of mono- or oligonucleotides provided sequentially by different solutions (A, T, G, C) into strands that are replicated in a nanoball (NB) at an electrode.

First claim

1 . An apparatus for the processing of nucleotide sequences, comprising:
an array of electrodes; and at least one nanoball comprising replications of a nucleotide sequence of interest, wherein said nanoball is attached to an electrode to which not more than one nanoball of that size can be attached, wherein electrical potentials are selectively applied to the electrodes of the array in order to attract and/or repel nanoballs and/or other components.

2 . A method for the processing of nucleotide sequences,
wherein at least one nanoball comprising replications of a nucleotide sequence of interest is attached to an electrode of an array of electrodes to which not more than one nanoball of that size can be attached, wherein electrical potentials are selectively applied to the electrodes of the array in order to attract and/or repel nanoballs and/or other components.

3 . The apparatus of claim 1 ,
wherein the inner diameter of the nanoball is larger than about 40% of the inner diameter of the associated electrode.

4 . The apparatus of claim 1 ,
wherein it comprises a container with a reaction chamber in which the array of electrodes is located, said container having an inlet to which at least two different reagent reservoirs can selectively be coupled.

5 . The apparatus of claim 4 ,
wherein the reagent reservoirs comprise solutions (A, T, G, C) with different dielectric characteristics.

6 . The apparatus of claim 1 ,
wherein it comprises a processing circuit ( 130 ) that allows the selective application of electrical potentials to the electrodes.

7 . The apparatus of claim 1 ,
wherein the electrodes of the array are exposed to a plurality of nanoballs comprising replications of nucleotide sequences of interest, said nanoballs having sizes such that substantially only one of them can attach to one electrode at the same time.

8 . The apparatus of claim 1 ,
wherein the electrodes of the array are exposed to a plurality of nanoballs comprising replications of nucleotide sequences of interest, wherein said electrodes can be addressed individually or as ensembles to specifically attract said nanoballs from a supernatant solution.

9 . The apparatus of claim 1 ,
wherein the nanoball is produced by rolling circle amplification.

10 . (canceled)

11 . The apparatus of claim 1 ,
wherein the capacitance of electrodes is or can be measured.

12 . The apparatus of claim 11 ,
wherein binding of a nanoball to an electrode is or can be detected via the associated change of capacitance at said electrode.

13 . The apparatus of claim 11 ,
wherein additions of nucleotides and/or oligonucleotides to a nanoball attached to an electrode are or can be detected via the associated change of capacitance at said electrode.

14 . The apparatus of claim 1 ,
wherein the array of electrodes is sequentially exposed to different solutions (A, T, G, C) of mono- or oligonucleotides.

15 . Use of the apparatus of claim 1 for sequencing nucleic acids, molecular diagnostics, biological sample analysis, chemical sample analysis, food analysis, and/or forensic analysis.

Assignees

• Koninkl Philips Nv

Inventors

• Van De Stolpe Anja
• Feitsma Harma Martine
• Van Der Zaag Pieter Jan
• Wimberger-Friedl Reinhold
• Den Toonder Jacob Marinus Jan
• Pierik Anke
• Van Hemert Freek

Classifications

• G01N27/3275 Primary

  Sensing specific biomolecules, e.g. nucleic acid strands, based on an electrode surface reaction · CPC title

• G01N27/3278

  involving nanosized elements, e.g. nanogaps or nanoparticles (nanopores G01N33/48721; magnetic beads G01N27/745) · CPC title

• B82Y15/00 Primary

  Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors · CPC title

• B01J2219/00608

  DNA chips · CPC title

• B01J2219/00722

  Nucleotides · CPC title