VITRO EVOLUTION IN MICROFLUIDIC SYSTEMS

• US 20090197248A1
• Filed: 10/10/2005
• Published: 08/06/2009
• Est. Priority Date: 10/08/2004
• Status: Active Grant

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation), UK Research and Innovation
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Griffiths, Andrew David, Link, Darren, Weitz, David, Ahn, Keunho, Bibette, Jerome
• Granted Patent: US 9,029,083 B2
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: B01F 23/41 Emulsifying
• CPC Class Codes: B01F 25/433 Mixing tubes wherein the shape of the tube influences the mixing, e.g. mixing tubes with varying cross-section or provided with inwardly extending profiles
• CPC Class Codes: B01F 25/4331 Mixers with bended, curved, coiled, wounded mixing tubes or comprising elements for bending the flow
• CPC Class Codes: B01F 25/4338 Mixers with a succession of converging-diverging cross-sections, i.e. undulating cross-section
• CPC Class Codes: B01F 33/3011 using a sheathing stream of a fluid surrounding a central stream of a different fluid, e.g. for reducing the cross-section of the central stream or to produce droplets from the central stream
• CPC Class Codes: B01F 33/3021 the components to be mixed being combined in a single independent droplet, e.g. these droplets being divided by a non-miscible fluid or consisting of independent droplets
• CPC Class Codes: B01F 33/3031 using electro-hydrodynamic [EHD] or electro-kinetic [EKI] phenomena to mix or move the fluids
• 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 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/0052 in the shape of elongated tubes
• CPC Class Codes: B01J 2219/00545 Colours
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2200/0636 Focussing flows, e.g. to laminate flows
• CPC Class Codes: B01L 2200/0673 Handling of plugs of fluid surrounded by immiscible fluid
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0864 : comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
• CPC Class Codes: B01L 2300/0867 : Multiple inlets and one sample wells, e.g. mixing, dilution
• CPC Class Codes: B01L 2400/0415 : electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/0487 : fluid pressure, pneumatics
• CPC Class Codes: B01L 3/502746 : characterised by the means for controlling flow resistance, e.g. flow controllers, baffles B01L3/502738 takes precedence
• CPC Class Codes: B01L 3/502753 : characterised by bulk separation arrangements on lab-on-a-chip devices, e.g. for filtration or centrifugation separation in general B01D; microapparatus for analysis using electrophoresis G01N27/44791; sample preparation G01N1/28
• CPC Class Codes: B01L 3/502776 : specially adapted for focusing or laminating flows
• CPC Class Codes: B01L 3/502784 : specially adapted for droplet or plug flow, e.g. digital microfluidics automatic analysis using a stream of discrete samples in a tube system G01N35/08
• CPC Class Codes: C12N 15/1058 : Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
• CPC Class Codes: C12N 15/1075 : by coupling phenotype to genotype, not provided for in other groups of this subclass
• CPC Class Codes: C12P 21/00 : Preparation of peptides or proteins single cell protein C12N1/00
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 15/1459 : the analysis being performed on a sample stream
• CPC Class Codes: G01N 15/1484 : microstructural devices
• CPC Class Codes: G01N 15/149 : specially adapted for sorting particles, e.g. by their size or optical properties
• CPC Class Codes: G01N 2015/149 : Sorting the particles

Abstract

The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising the steps of: (a) compartmentalising genetic elements into microcapsules; and (b) sorting the genetic elements which express the gene product having the desired activity; wherein at least one step is under microfluidic control. The invention enables the in vitro evolution of nucleic acids and proteins by repeated mutagenesis and iterative applications of the method of the invention.

Claims

1. A method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising the steps of:

(a) compartmentalizing the genetic elements into microcapsules;

(b) sorting the genetic elements which express gene product (s) having the desired activity;

wherein at least one step is under microfluidic control.

2-84. -84. (canceled)

85. A method for compartmentalising a genetic element and expressing the genetic element to form its gene product within the compartment, comprising the steps of:

(a) forming an aqueous solution comprising the genetic element and the components necessary to express it to form its gene product;

(b) microencapsulating the solution so as to form a discrete microcapsule comprising the genetic element; and

(c) exposing the microcapsule to conditions suitable for the expression of the genetic element to form its gene product to proceed;

wherein at least one step is under microfluidic control.

86-95. -95. (canceled)

96. A method for preparing a gene product, comprising the steps of:

(a) preparing a genetic element encoding the gene product;

(b) compartmentalising genetic elements into microcapsules;

(c) expressing the genetic elements to produce their respective gene microcapsules;

(d) expressing the genetic elements to produce their respective gene products within the microcapsules;

(e) sorting the genetic elements which produce the gene product (s) having the desired activity; and

(f) expressing the gene product having the desired activity;

wherein at least one step is under microfluidic control.

97. A method for screening a compound or compounds capable of modulating the activity of a gene product, comprising the steps of:

(a) preparing a repertoire of genetic elements encoding gene product;

(b) compartmentalising the genetic elements into microcapsules;

(c) expressing the genetic elements to produce their respective gene products within the microcapsules;

(d) sorting the genetic elements which produce the gene product (s) having the desired activity; and

(e) contacting a gene product having the desired activity with the compound or compounds and monitoring the modulation of an activity of the gene product by the compound or compounds;

wherein at least one step is under microfluidic control.

98. A method for preparing a compound or compounds comprising the steps of:

(a) providing a synthesis protocol wherein at least one step is facilitated by a polypeptide;

(b) preparing genetic elements encoding variants of the polypeptide which facilitates this step;

(c) compartmentalising the genetic elements into microcapsules;

(d) expressing the genetic elements to produce their respective gene products within the microcapsules;

(e) sorting the genetic elements which produce polypeptide gene product (s) having the desired activity; and

(f) preparing the compound or compounds using the polypeptide gene product identified in (e) to facilitate the relevant step of the synthesis;

wherein at least one step is under microfluidic control.

99. A method for preparing a gene product, comprising the steps of:

(a) preparing a genetic element encoding the gene product;

(b) compartmentalising genetic elements into microcapsules;

(c) expressing the genetic elements to produce their respective gene products within the microcapsules;

(d) sorting the genetic elements which produce the gene product (s) having the desired activity using a change in their optical properties; and

(e) expressing the gene product having the desired activity;

wherein at least one step is under microfluidic control.

100. A method for screening a compound or compounds capable of modulating the activity of a gene product, comprising the steps of:

(a) preparing a repertoire of genetic elements encoding gene product;

(b) compartmentalising the genetic elements into microcapsules;

(c) expressing the genetic elements to produce their respective gene products within the microcapsules;

(d) sorting the genetic elements which produce the gene product (s) having the desired activity using a change in their optical properties; and

(e) contacting a gene product having the desired activity with the compound or compounds and monitoring the modulation of an activity of the gene product by the compound or compounds;

wherein at least one step is under microfluidic control.

101. A method for preparing a compound or compounds comprising the steps OF:

(a) providing a synthesis protocol wherein at least one step is facilitated by a polypeptide;

(b) preparing genetic elements encoding variants of the polypeptide which facilitates this step;

(c) compartmentalising the genetic elements into microcapsules;

(d) expressing the genetic elements to produce their respective gene products within the microcapsules;

(e) sorting the genetic elements which produce polypeptide gene product (s) having the desired activity using a change in their optical properties; and

(f) preparing the compound or compounds using the polypeptide gene product identified in (e) to facilitate the relevant step of the synthesis;

wherein at least one step is under microfluidic control.

102. A method for preparing a gene product, comprising the steps of:

(a) preparing a genetic element encoding the gene product;

(b) expressing the genetic elements to produce their respective gene products such that the gene products are linked to the genetic elements encoding them;

(c) compartmentalising genetic elements into microcapsules;

(d) sorting the genetic elements which produce the gene product(s) having the desired activity; and

(e) expressing the gene product having the desired activity;

wherein at least one step is under microfluidic control.

103. A method for screening a compound or compounds capable of modulating the activity of a gene product, comprising the steps of:

(a) preparing a genetic element encoding the gene product;

(b) expressing the genetic elements to produce their respective gene products and linking the gene products to the genetic elements encoding them;

(c) compartmentalising genetic elements into microcapsules;

(d) sorting the genetic elements which produce the gene product(s) having the desired activity; and

(e) contacting a gene product having the desired activity with the compound or compounds and monitoring the modulation of an activity of the gene product by the compound or compounds;

wherein at least one step is under microfluidic control.

104. A method for preparing a compound or compounds comprising the steps of:

(a) providing a synthesis protocol wherein at least one step is facilitated by a polypeptide;

(b) preparing genetic elements encoding variants of the polypeptide which facilitates this step;

(c) expressing the genetic elements to produce their respective gene products such that the gene products are linked to the genetic elements encoding them;

(d) compartmentalising the genetic elements into microcapsules;

(e) sorting the genetic elements which produce polypeptide gene product(s) having the desired activity; and

(f) preparing the compound or compounds using the polypeptide gene product identified in (e) to facilitate the relevant step of the synthesis;

wherein at least one step is under microfluidic control.

105. A method for preparing a gene product, comprising the steps of:

(a) preparing a genetic element encoding the gene product;

(b) expressing the genetic elements to produce their respective gene products;

(c) compartmentalising genetic elements into microcapsules;

(d) sorting the genetic elements which produce the gene product(s) having the desired activity using a change in their optical properties; and

(e) expressing the gene product having the desired activity;

wherein at least one step is under microfluidic control.

106. A method for screening a compound or compounds capable of modulating the activity of a gene product, comprising the steps of:

(a) preparing a genetic element encoding the gene product;

(b) expressing the genetic elements to produce their respective gene products;

(c) compartmentalising genetic elements into microcapsules;

(d) sorting the genetic elements which produce the gene product(s) having the desired activity using a change in their optical properties; and

(e) contacting a gene product having the desired activity with the compound or compounds and monitoring the modulation of an activity of the gene product by the compound or compounds;

wherein at least one step is under microfluidic control.

107. A method for preparing a compound or compounds comprising the steps of:

(a) providing a synthesis protocol wherein at least one step is facilitated by a polypeptide;

(b) preparing genetic elements encoding variants of the polypeptide which facilitates this step;

(c) expressing the genetic elements to produce their respective gene products;

(d) compartmentalizing the genetic elements into microcapsules;

(e) sorting the genetic elements which produce polypeptide gene product(s) having the desired activity using a change in their optical properties; and

(f) preparing the compound or compounds using the polypeptide gene product identified in (e) to facilitate the relevant step of the synthesis;

wherein at least one step is under microfluidic control.