PROCESS FOR SELF-ASSEMBLY OF STRUCTURES IN A LIQUID

• US 20080241836A1
• Filed: 03/31/2008
• Published: 10/02/2008
• Est. Priority Date: 08/07/2006
• Status: Abandoned Application

• Current Assignee: Gafur Zainiev, Inlik Zainiev, Timur Zainiev
• Original Assignee: Gafur Zainiev, Inlik Zainiev, Timur Zainiev
• Inventors: Zainiev, Gafur, Zainiev, Inlik, Zainiev, Timur
• Application Number:
  US11/927,891
• Publication Number:
  US 20080241836A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides

Abstract

A process and apparatus for self-assembling a number of elements and determining their sequence is provided. In the field of DNA analysis, an iterative process is disclosed wherein an apparatus with a set of reaction chambers in which a species of recognition element nucleotides are differentially added and subjected to a polymerization reaction allows recognition of which species is next in sequence on a template strand by the effect that synthesis has on a detecting template as measured by a detector in a detection area. Stepwise addition of the identified species then determines if an element repeat exists. The process is repeated until the entire structure is complete and the sequence identified.

Claims

1. A process of self-assembling a number of elements into a structure comprising:

providing N recognition chambers,

adding a plurality of sequencing templates into a solution present in each chamber of said N recognition chambers;

adding a plurality of detecting templates into said solution present in each chamber of said N recognition chambers;

introducing a unique plurality of a homogeneous species of recognition elements to each chamber of said N recognition chambers;

exposing said plurality of templates and said unique plurality of recognition elements in each of said N recognition chambers to a polymerization reaction with a plurality of polymerization enzymes in each of said N recognition chambers;

identifying a next in sequence recognition element on said plurality of templates in at least one of said N recognition chambers;

repeating the introducing through subjecting steps until said structure is complete;

placing building elements corresponding to said next in sequence recognition element in at least one of said N recognition chambers; and

subjecting said plurality of templates and said building elements to said polymerization reaction in at least one of said N recognition chambers.

2. The process of claim 1, further comprising determining said template sequence.

3. The process of claim 1 wherein said recognition chamber further comprises a reactor area and a detection area.

4. The process of claim 3 wherein said detection template is immobilized in one of said detection area and said reactor area.

5. The process of claim 3 wherein a capture agent is immobilized in said detection area.

6. The process of claim 1 wherein said identifying a next in sequence recognition element further comprises detecting synthesis of complementary structure to said detection template.

7. The process of claim 1, further comprising:

placing in a repeat detecting chamber at least said plurality of sequencing templates and said solution wherein detecting repeat elements occurs by stepwise addition of building elements or recognition elements corresponding to said next in sequence recognition element;

transferring said solution from all N recognition chambers to said repeat detecting chamber prior to adding said building elements or recognition elements; and

calculating the number of repeat elements in the sequence of said template.

8. The process of claim 7, further comprising:

transferring said solution from said N recognition chambers and said solution from said repeat detection chamber to a sequence construction chamber; and

adding building elements corresponding to said next in sequence recognition element to said at least one of said N recognition chambers.

9. The process of claim 1 wherein said solution further comprises a primer sequence covalently hybridized to one of said plurality of sequencing templates or detecting templates.

10. The process of claim 1, wherein said unique plurality of recognition elements further comprise a label.

11. An apparatus for self-assembly of a number of elements comprising:

a reaction area;

a preparation area in fluidic connection with said reaction area;

a detection area in fluidic, physical, or optical connection with said reaction area;

said reaction area having no moving parts;

said reaction area having N recognition chambers;

each chamber having a plurality of microdispensers, each of said microdispensers capable of dispensing a unique species of recognition element or building element.

12. The apparatus of claim 11, where N is 4.

13. The apparatus of claim 11, further comprising a repeat detecting chamber.

14. The apparatus of claim 13, wherein said repeat detecting chamber is in fluidic connection with said recognition chambers and further comprising a sequence construction chamber in fluidic connection with said recognition chambers and said repeat detecting chamber.