Methods and Apparatus for Assembly

• US 20140018441A1
• Filed: 07/12/2013
• Published: 01/16/2014
• Est. Priority Date: 07/12/2012
• Status: Active Grant

• Current Assignee: Massachusetts Institute of Technology
• Original Assignee: Massachusetts Institute of Technology
• Inventors: Fracchia, Charles, Gershenfeld, Neil, Cheung, Kenneth
• Granted Patent: US 9,073,962 B2
• Time in Patent Office: Days
• US Class Current: 514/777
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical

Abstract

In exemplary implementations of this invention, hierarchical, nanometer-precise assembly is performed: A first structural unit is attached to a solid substrate in a first fluidic flow. A second structural unit is attached to the first structural unit in a second fluidic flow, a third structural unit is attached to the second structural unit in a third fluidic flow, and so on, until a target structure comprising the structural units is assembled. The first, second, third and so on fluidic flows are separate and occur in order in a temporal sequence. During the temporal sequence, a specific permutation of nucleobases is used repeatedly, in separate fluidic flows which occur at different times, to form multiple attachments between structural units in an assembly. The assembled target structure is removed from the solid substrate. Attachments between the structural units may be formed by nucleobase pairing.

Claims

1. A method comprising the following steps, in combination:

(a) attaching a first structural unit to a solid substrate in a first fluidic flow;

(b) attaching a second structural unit to the first structural unit in a second fluidic flow, attaching a third structural unit to the second structural unit in a third fluidic flow, and so on, until a target structure comprising the structural units is assembled, the first, second, third and so on fluidic flows being separate and occurring in order in a temporal sequence; and

(c) removing the target structure from the solid substrate;

wherein

(i) attachments between structural units are formed by nucleobase pairing, and

(ii) during the temporal sequence, a specific attachment permutation is used repeatedly, in separate fluidic flows which occur at different times, to form multiple attachments between structural units in an assembly sequence.

2. The method of claim 1, wherein:

(a) the target structure, when assembled, includes a physical sequence of structural units; and

(b) overall direction of the physical sequence varies as a function of position; and

(c) a majority of the changes of the overall direction consist of 90 degree turns.

3. The method of claim 1, wherein each attachment site on a structural unit comprises three elongated structures that are encoded with nucleobases for selective docking with other structural units.

4. The method of claim 3, further comprising the step of attaching or confining a payload to or in the target structure, which payload does not consist of the structural units.

5. The method of claim 1, wherein:

(a) attachment between structural units occurs at or adjacent to attachment sites on the structural units; and

(b) a structural unit includes exactly four attachment sites.

6. The method of claim 1, wherein one or more attachments between structural units are dynamically reconfigurable.

7. The method of claim 5, wherein nucleic acid strand displacement is employed to activate attachment sites.

8. The method of claim 1, wherein one or more nucleobases used in the nucleobase pairing are unnatural.

9. The method of claim 1, further comprising using sensor measurements to assess yield or other metrics of an assembly step.

10. The method of claim 1, further comprising using microscopy imaging of fluorescence from FRET fluorophores to assess yield or other metrics of an assembly step.

12. The method of claim 1, wherein:

(a) a structural unit has a main body; and

(b) overall shape of an external planar face of the main body, not including any elongated protrusions from the main body, is a parallelogram.

13. The method of claim 1, wherein, when the target structure is assembled, a plurality of structural units are connected in-plane.

11. The method of claim 11, wherein light, or lack thereof, from three distinct fluorophore pairs is indicative of whether an assembly step yielded a right turn, left turn, go straight, or no connection.

14. A system comprising, in combination:

(a) a microfluidic growth chamber;

(b) one or more valves configured for controlling movement of fluid to the growth chamber, including materials suspended, positioned or dissolved in the fluid;

(c) tangible machine-readable media; and

(d) one or more processors;

wherein

(i) the tangible machine-readable media encode instructions for the one or more processors to control an assembly process, which assembly process occurs in the growth chamber and comprises attaching a second structural unit to a first structural unit in a first fluidic flow, attaching a third structural unit to the second structural unit in a second fluidic flow, and so on, until a target structure comprising the structural units is assembled, wherein the first, second, and so on fluidic flows are separate and occur in order in a temporal sequence,

(ii) attachments between structural units are formed by nucleobase pairing, and

(iii) during the temporal sequence, a specific attachment permutation is used repeatedly, in separate fluidic flows which occur at different times, to form multiple attachments between structural units in an assembly sequence.

15. The system of claim 14, further comprising a microscopy imager for measuring fluorescence from FRET fluorophores to assess yield or other metrics of an assembly step.

16. The system of claim 14, wherein:

(a) the target structure, when assembled, includes a physical sequence of structural units; and

(b) overall direction of the physical sequence varies as a function of position; and

(c) one or more changes of the overall direction consist of 108 degree turns.

17. The system of claim 14, wherein each attachment site on a structural unit comprises three elongated structures that are encoded with nucleobases for selective docking with other structural units.

18. An article of manufacture comprising a plurality of structural units, wherein:

(a) each of the structural units, respectively, includes a main body and two or more attachment sites, each of the attachment sites comprising three elongated structures that protrude from the main body;

(b) attachments between structural units are formed by nucleobase pairing; and

(c) for each respective nucleobase pair participating in the nucleobase pairing that joins structural units, one nucleobase in the respective pair is part of a first attachment site of a first structural unit and the other nucleobase in the respective pair is part of a second attachment site in a second structural unit or is positioned between the first and second attachment sites.

19. The article of manufacture of claim 18, wherein the article of manufacture is configured to attach to, or confine, a payload.

20. The article of manufacture of claim 19, wherein the article of manufacture includes the payload.