Real Time Microarrays

Abstract

This invention provides methods and systems for measuring the binding of analytes in solution to probes bound to surfaces in real-time.

1 .- 66 . (canceled) 
     
     
         67 . A system for determining at least one parameter associated with a binding interaction between at least one analyte and at least one probe, comprising:
 a substrate comprising a surface having said at least one probe coupled to said surface;   a signal source that provides an input signal to said surface;   a chamber in fluid communication with said surface, wherein during use, said chamber retains a fluid comprising said at least one analyte under conditions that are sufficient to permit said binding interaction between said at least one analyte and said at least one probe;   a detector that detects output signals from said surface in response to said input signal from said signal source, which output signals are detected at multiple time points in real time during said binding interaction and are indicative of said binding interaction; and   a controller in communication with said detector, wherein said controller (i) determines said at least one parameter associated with said binding interaction based at least in part on said output signals from said detector, and (ii) provides an output indicative of said at least one parameter.   
     
     
         68 . The system of  claim 67 , further comprising an electronic storage device that stores said output. 
     
     
         69 . The system of  claim 67 , wherein said at least one probe provides a fluorescence signal, a luminescence signal, or an absorption signal. 
     
     
         70 . The system of  claim 67 , wherein said at least analyte provides a fluorescence signal, a luminescence signal, or an absorption signal. 
     
     
         71 . The system of  claim 67 , wherein said input signal is an electromagnetic signal. 
     
     
         72 . The system of  claim 67 , wherein said at least one parameter comprises:
 a forward binding reaction rate;   a backward binding reaction rate;   C which is an original quantity of said at least one analyte in said fluid;   C−(P o −P(t)) which is an available analyte density at time t, wherein P o  is a number of unbound molecules of said at least one probe, and wherein P(t) is a number of unbound molecules of said at least one probe at time t;   t which is a time constant;   P ∞  which is a steady-state value of P(t);   n(t), which is a number of analytes in said fluid that are specific to said probe molecule;   P near , which is a probability that said at least one analyte is in close proximity to said probe molecule;   P h , which is a probability that, in a unit interval of time, said at least one analyte binds to said probe once said analyte is near;   P r , which is a probability that, in a unit interval of time, said at least one analyte bound to said probe molecule is released;   N, which is a total number of analyte molecules;   q(t), which is a number of unbound molecules of said at least one analyte as a function of time;   a reaction rate between said at least one analyte and said at least one probe; and   a cross-hybridization parameter.   
     
     
         73 . The system of  claim 67 , wherein said substrate comprises a plurality of different probes coupled to said surface. 
     
     
         74 . The system of  claim 67 , wherein said fluid is configured to contain a plurality of different analytes, including said at least one analyte. 
     
     
         75 . The system of  claim 67 , wherein said at least one probe is labeled with a donor. 
     
     
         76 . The system of  claim 67 , wherein said at least one analyte is labeled with an acceptor. 
     
     
         77 . The system of  claim 76 , wherein said acceptor is a quencher. 
     
     
         78 . The system of  claim 67 , wherein said at least one analyte is not labeled with a metal cluster. 
     
     
         79 . The system of  claim 67 , wherein said binding interaction is non-competitive. 
     
     
         80 . The system of  claim 67 , wherein during use, said output signals are detected while said fluid is in contact with said surface. 
     
     
         81 . The system of  claim 80 , wherein during use, said output signals are detected by said detector without washing said fluid from surface. 
     
     
         82 . The system of  claim 67 , wherein said surface comprises a plurality of probe spots, and wherein a given probe spot of said plurality of probe spots includes said at least one probe. 
     
     
         83 . The system of  claim 67 , wherein during use, said output signals are generated in the absence of fluorescent resonance energy transfer. 
     
     
         84 . The system of  claim 67 , wherein said detector is integrated with said substrate. 
     
     
         85 . The system of  claim 67 , wherein said signal source and said detector are disposed adjacent to a same side of said substrate. 
     
     
         86 . The system of  claim 67 , wherein during use, said fluid comprises a plurality of different analytes. 
     
     
         87 . The system of  claim 67 , further comprising an assembly that is capable of changing a temperature of said fluid and/or said substrate.