Methods and systems for microfluidic screening

Abstract

Provided are methods and systems useful for screening large libraries of effector molecules. Such methods and systems are particularly useful in microfluidic systems and devices. The methods and systems provided herein utilize encoded effectors to screen large libraries of effectors.

1 . A method for screening an encoded effector, the method comprising:
 (a) providing at least one cell and a scaffold in an encapsulation, wherein the scaffold comprises an encoded effector bound to the scaffold by a photocleavable linker and a nucleic acid encoding the effector;   (b) cleaving the photocleavable linker to release the encoded effector from the scaffold; and   (c) detecting a signal from the droplet, wherein the signal results from an interaction between the encoded effector and the at least one cell.   
     
     
         2 . The method of  claim 1 , wherein cleaving the photocleavable linker releases a pre-determined amount of the encoded effector into the droplet. 
     
     
         3 . The method of  claim 1 , wherein the photocleavable linker is cleaved using electromagnetic radiation. 
     
     
         4 . The method of  claim 1 , wherein cleaving the photocleavable linker comprises exposing the encapsulation to a light from a light source. 
     
     
         5 . The method of  claim 4 , wherein the light intensity of the light is from about 0.01 J/cm 2  to about 200 J/cm 2 . 
     
     
         6 . The method  claim 1 , further comprising the step of lysing the one or more cells. 
     
     
         7 . The method of  claim 1 , further comprising providing an activating reagent to activate the photocleavable linker, so as to enable the photocleavable linker to be cleaved from the encoded effector. 
     
     
         8 . A system for screening an encoded effector, the system comprising:
 (a) one or more cells;   (b) a scaffold, wherein an encoded effector is bound to the scaffold by a cleavable linker, wherein a nucleic acid encoding the effector is bound to the scaffold; and   (c) a microfluidic device configured to:
 (i) receive the one or more cells and scaffold; 
 (ii) encapsulate the one or more cells and scaffold within an encapsulation; 
 (iii) cleave the cleavable linker from the encoded effector to release a predetermined amount of the encoded effector within the encapsulation; 
 (iv) incubate the encoded effector with the one or more cells for a period of time; 
 (v) detect a signal from the encapsulation, wherein the signal results from an interaction between the encoded effector and one or more cells; and 
 (vi) sort the encapsulation based on the detection of the signal. 
   
     
     
         9 . The system of  claim 8 , wherein the cleavable linker is a photocleavable linker. 
     
     
         10 . The system of  claim 8 , wherein the microfluidic device further comprises a first collection tube and second collection tube for sorting the encapsulation, wherein the encapsulation is placed in 1) the first collection tube if the signal is at or above a predetermined threshold or 2) the second collection tube if the signal is below a predetermined threshold. 
     
     
         11 . The system of  claim 10 , further comprising a waveform pulse generator to move the encapsulation to the first or second collection tube by an electrical field gradient, by sound, by a diaphragm, by modifying geometry of the microfluidic channel, or by changing the pressure of a microfluidic channel of the microfluidic device. 
     
     
         12 . The system of  claim 10 , wherein the signal is detected based on detecting morphological changes in the one or more cells measured by recording a series of images of the droplet or detecting fluorescence emitted by a molecular beacon or probe. 
     
     
         13 . The system of  claim 8 , wherein the period of time is controlled by residence time as the encapsulation travels through a microfluidic channel of the microfluidic device. 
     
     
         14 . A method for amplifying a primer to maximize cellular nucleic acid capture comprising:
 (a) providing an encapsulation comprising a nucleic acid encoded scaffold with one or more cells, an amplification mix, and a nicking enzyme, wherein a nucleic acid encoding is bound to the nucleic acid encoded scaffold;   (b) lysing the one or more cells to release one or more cellular nucleic acids;   (c) nicking the nucleic acid encoding with the nicking enzyme, thereby creating an encoded nucleic acid primer;   (d) amplifying the encoded nucleic acid primer via the nicking site and amplification mix; and   (e) labeling a released cellular nucleic acid with the encoded nucleic acid primer.   
     
     
         15 . The method of  claim 14 , wherein the specific site comprises a specific nucleotide sequence. 
     
     
         16 . The method of claim of  claim 14 , wherein amplifying the encoded nucleic acid primer comprises 1) creating a copy of the nucleic acid encoding that extends from the nicking site, and 2) nicking the nucleic acid encoding copy to create another encoded nucleic acid primer. 
     
     
         17 . The method of claim of  claim 14 , wherein amplifying the encoded nucleic acid primer comprises simultaneously 1) creating a copy of the nucleic acid encoding that extends from the nicking site, and 2) displacing the nucleic acid encoding copy to create another encoded nucleic acid primer. 
     
     
         18 . The method of  claim 17 , wherein the amplification mix comprises an amplification enzyme, such that the amplification enzyme enables for a copy of the nucleic acid encoding to be simultaneously created and displaced. 
     
     
         19 . The method of  claim 18 , wherein the amplification enzyme comprises a polymerase. 
     
     
         20 . The method of  claim 14 , wherein each nucleic acid encoding comprises a capture site that prescribes a target cellular coding or a target cellular nucleic acid to label a released cellular nucleic acid.