Single molecule loading methods and compositions

• US 8,906,831 B2
• Filed: 03/30/2009
• Issued: 12/09/2014
• Est. Priority Date: 03/31/2008
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Eid, John, Turner, Stephen, Dalal, Ravi, Flusberg, Benjamin, Korlach, Jonas, Lin, Steven, Fehr, Adrian, Christians, Fred, Emig, Robin, Gray, Jeremy, Sebra, Robert, Sun, Lei, Dudek, Stephen
• Primary Examiner(s): Babic, Christopher M
• Assistant Examiner(s): Flinders, Jeremy C
• Application Number:
  US12/384,097
• Publication Number:
  US 20100009872A1
• Time in Patent Office: 2,080 Days
• US Class Current: 506/16
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: C12N 2310/50 Physical structure
• CPC Class Codes: C12N 2310/51 in polymeric form, e.g. multimers, concatemers
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2521/543 Immobilised enzyme(s)
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: G01N 33/54313 the carrier being characterised by its particulate form
• CPC Class Codes: G01N 33/54366 Apparatus specially adapted for solid-phase testing

Abstract

Methods for non-random loading of single analyte molecules into array structures are provided. The methods allow for distribution of a population of target molecules into a plurality of size confined regions such as wells. Sizing moieties are linked to individual target molecules. The sizing moieties are of sufficient size, relative to the size-confined reaction or observation regions, such that only a selected number of sizing moieties will fit into the size confined regions. The confined regions and the sizing moieties or target molecules comprise a selected charge that allow for controlling the loading of the sizing moities.

Claims

1. A method of distributing a population of target molecules into a plurality of size confined reaction or observation regions, the method comprising:

providing a structure comprising the plurality of size confined reaction or observation regions, wherein such regions comprise wells;

providing the population of target molecules to be distributed;

linking at least one nucleic acid sizing moiety to individual target molecules, wherein the sizing moieties are of sufficient size, relative to the size-confined reaction or observation regions, such that only a single sizing moiety will fit into each size confined region, thereby preventing the entry of an additional sizing moiety; and

,

loading the target molecules into the regions such that the size of the confined regions results in a single target molecule distributed into each region, thereby distributing the population of target molecules into the plurality of size confined regions.

2. The method of claim 1, wherein the size confined regions are optically confined.

3. The method of claim 1, wherein the sizing moieties expand upon binding to structures in the confined regions, thereby preventing additional sizing moieties from entering into the confined regions.

4. The method of claim 1, wherein individual sizing moieties are non-covalently linked to individual target molecules of the confined regions.

5. The method of claim 4, wherein the target molecules are polymerase enzyme molecules that comprise a reactive or binding moiety that permits attachment of the sizing moiety.

7. The method of claim 1 wherein the wells comprise zero-mode waveguides (ZMWs).

8. The method of claim 7 wherein the ZMWs have diameters of about 20 nm to about 200 nm.

9. The method of claim 1 wherein the nucleic acid sizing moiety comprises a cloned nucleic acid (DNA or RNA), an expressed nucleic acid, a genomic nucleic acid, an amplified nucleic acid or a cDNA.

10. The method of claim 1 wherein the nucleic acid sizing moiety has a single binding moiety.

11. The method of claim 1 wherein the nucleic acid sizing moiety comprises a self-assembled DNA structure.

12. The method of claim 1 wherein the single target molecules comprise polymerase enzymes.

6. A method of distributing a population of target molecules into a plurality of wells in a small well array, the method comprising:

providing the small well array, which array comprises the plurality of wells, which wells individually comprise a reaction or observation region;

providing a population of nucleic acid particles that comprise, bind, or package a single target molecule, wherein the plurality of wells individually are configured to receive a single particle from the population of particles into the reaction or observation region of the well wherein the nucleic acid particles prevents the entry of additional nucleic acid particles; and

;

delivering the population of particles into the plurality of wells, thereby distributing a single target molecule into the plurality of wells of the small well array.

13. A method of distributing a population of target molecules into a plurality of size confined reaction or observation regions, the method comprising:

providing a structure comprising the plurality of size confined reaction or observation regions, wherein such regions comprise wells;

providing the population of target molecules to be distributed;

linking at least one nucleic acid sizing moiety to individual target molecules, wherein the sizing moieties are of sufficient size, relative to the size-confined reaction or observation regions, so that only a selected number of sizing moieties will fit into the size confined regions, wherein the nucleic acid sizing moiety comprises DNA origami; and

,

loading the target molecules into the regions such that the size of the confined regions results in a single target molecule distributed into each region, thereby distributing the population of target molecules into the plurality of size confined regions.

14. The method of claim 13 wherein the nucleic acid sizing moiety comprises a single polymerase binding site.

15. The method of claim 13 wherein the nucleic acid sizing moiety is made by the polymerase enzyme target molecule.