Generation of uniform fragments of nucleic acids using patterned substrates
AssigneeIllumina, Inc.
InventorsKevin Gunderson, Michal Lebl, David L. Heiner
Life of this patent
Estimating the term…
Abstract
Methods of generating nucleic acid fragments of substantially uniform length from sample nucleic acids comprising linearly stretching the sample nucleic acids over a substrate having a plurality of cleavage regions separated by relatively consistent distances, cleaving the linearly stretched sample nucleic acids at the cleavage regions, and collecting the resulting nucleic acid fragments. The method may further include collecting and concentrating the resultant nucleic acid fragments of substantially uniform length.
Claims19
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising contacting one or more sample nucleic acids with an affinity ligand, linearly stretching the one or more sample nucleic acids over a substrate including a modified region comprising a plurality of affinity ligand receptors and a plurality of cleavage regions separated by relatively consistent distances, and cleaving the linearly stretched one or more sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions.
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising linearly stretching the one or more nucleic acids over a substrate comprising a plurality of cleavage regions separated by relatively consistent distances, and cleaving the one or more linearly stretched sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, further comprising linearly stretching the one or more nucleic acids over the substrate by surface-tethered nucleic acid stretching, further comprising attaching a micron-size bead to the free end of the nucleic acid.
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising linearly stretching the one or more nucleic acids over a substrate comprising a plurality of cleavage regions separated by relatively consistent distances, and cleaving the one or more linearly stretched sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, further comprising linearly stretching the one or more nucleic acids over the substrate by surface-tethered nucleic acid stretching, further comprising attaching a magnetic bead to the nucleic acid and using magnets for the nucleic acid stretching.
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising linearly stretching the one or more nucleic acids over a substrate comprising a plurality of cleavage regions separated by relatively consistent distances, and cleaving the one or more linearly stretched sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, wherein the linear stretching of the sample nucleic acid comprises a nucleic acid optical entrapment technique with an optically trapped particle attached to the sample nucleic acid.
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising linearly stretching the one or more nucleic acids over a substrate comprising a plurality of cleavage regions separated by relatively consistent distances, and cleaving the one or more linearly stretched sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, wherein the linear stretching of the sample nucleic acid comprises electrophoresis of nucleic acid.
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising linearly stretching the one or more nucleic acids over a substrate comprising a plurality of cleavage regions separated by relatively consistent distances, and cleaving the one or more linearly stretched sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, wherein the chemical cleavage agent comprises at least one chemical hydroxyl radical generator.
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising linearly stretching the one or more nucleic acids over a substrate comprising a plurality of cleavage regions separated by relatively consistent distances, and cleaving the one or more linearly stretched sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, wherein at least one of said one or more samples has a complexity of at least 1 Gbases.
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising contacting one or more sample nucleic acids with an affinity ligand, linearly stretching the one or more sample nucleic acids over a substrate including a modified region comprising a plurality of affinity ligand receptors and a plurality of cleavage regions separated by relatively consistent distances, and cleaving the linearly stretched one or more sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, wherein the cleavage regions comprise an electrode.
A method of generating nucleic acid fragments of substantially uniform length from one or more sample nucleic acids, comprising contacting one or more sample nucleic acids with an affinity ligand, linearly stretching the one or more sample nucleic acids over a substrate including a modified region comprising a plurality of affinity ligand receptors and a plurality of cleavage regions separated by relatively consistent distances, and cleaving the linearly stretched one or more sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, wherein said cleavage regions are activatable.
A method of sequencing nucleic acid, comprising linearly stretching one or more sample nucleic acids over a substrate comprising a plurality of cleavage regions separated by a uniform pitch, cleaving the linearly stretched one or more sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, thereby producing a substantially uniform length nucleic acid fragment pool, collecting the substantially uniform length nucleic acid fragment pool;
- and sequencing the resultant substantially uniform length nucleic acid fragment pool.
A method of sequencing nucleic acid, comprising linearly stretching one or more sample nucleic acids over a substrate comprising a plurality of cleavage regions separated by a uniform pitch, cleaving the linearly stretched one or more sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, thereby producing a substantially uniform length nucleic acid fragment pool, collecting the substantially uniform length nucleic acid fragment pool;
- and sequencing the resultant substantially uniform length nucleic acid fragment pool, wherein the cleavage regions comprise an electrode.
A method of sequencing nucleic acid, comprising linearly stretching one or more sample nucleic acids over a substrate comprising a plurality of cleavage regions separated by a uniform pitch, cleaving the linearly stretched one or more sample nucleic acids with a chemical cleavage agent that is directly attached to the substrate at the cleavage regions or nuclease that is directly attached to the substrate at the cleavage regions, thereby producing a substantially uniform length nucleic acid fragment pool, collecting the substantially uniform length nucleic acid fragment pool;
- and sequencing the resultant substantially uniform length nucleic acid fragment pool, wherein said cleavage regions are activatable.
Dependencies are inferred from the claim text.