Polynucleotide probe design

Abstract

An approach to designing a polynucleotide probe to hybridize selectively to a target polynucleotide sequence involves calculating the final concentration of the intended binding product between a candidate probe and the target sequence. The calculation takes into consideration the binding reaction between the candidate probe and the target fragment on the target sequence, as well as various other binding reactions, involving either the probe or the target fragment, that interfere with the intended binding reaction. In contrast to the conventional technology, which attempts to determine the entire structure of the target polynucleotide, this approach only needs to determine the binding dynamics that impact on the intended probe-target fragment binding. The approach does not require determination of the structure of the involved sequences.

1 . A method for obtaining information on how effectively a nucleotide probe selectively binds a target fragment in a target nucleotide sequence in a sample, comprising:
 (a) examining the target sequence for fragments capable of binding to the target fragment or the probe;   (b) generating equations to represent the binding reaction between the probe and the target fragment and the binding reactions identified in step (a); and   (c) solving the equations, for a lapsed time, to determine the concentration of the binding product between the probe and the target fragment,   
       wherein at least one of the steps is performed by a computer. 
     
     
         2 . The method of  claim 1 , wherein the binding reactions identified in step (a) include at least one involving at least part of the target fragment. 
     
     
         3 . The method of  claim 1 , wherein the binding reactions identified in step (a) include at least one involving at least part of the probe. 
     
     
         4 . The method of  claim 2 , wherein the at least one binding reaction is intra-strand. 
     
     
         5 . The method of  claim 2 , wherein the at least one binding reaction is inter-strand. 
     
     
         6 . The method of  claim 1 , wherein step (a) further comprises examining a plurality of polynucleotides in the sample for fragments capable of binding to the target fragment or the probe. 
     
     
         7 . The method of  claim 1 , wherein the generation of the equations comprises computing equilibrium rates of the bindings. 
     
     
         8 . The method of  claim 7 , wherein the equilibrium rates are computed with a nearest neighbor algorithm. 
     
     
         9 . The method of  claim 1 , wherein the generation of the equations comprises computing kinetic rates of the bindings. 
     
     
         10 . The method of  claim 1 , wherein the equations are ordinary differential equations or stochastic simulation equations. 
     
     
         11 . The method of  claim 1 , wherein the equations comprise concentrations of one or more of the polynucleotides of the plurality. 
     
     
         12 . The method of  claim 1 , wherein the probe is a primer, a hybridization probe, an siRNA or an antisense polynucleotide. 
     
     
         13 . The method of  claim 1 , wherein the sample is a cell. 
     
     
         14 . A computer system for obtaining information on how effectively a nucleotide probe selectively binds a target fragment in a target nucleotide sequence in a sample, said system comprising a processor, a memory and program code which, when executed by the processor, configures the system to:
 (a) examine the target sequence for fragments capable of binding to the target fragment or the probe;   (b) generate equations to represent the binding reaction between the probe and the target fragment and the binding reactions identified in step (a); and   (c) solve the equations, for a lapsed time, to determine the concentration of the binding product between the probe and the target fragment.   
     
     
         15 . A non-transitory computer-readable medium for obtaining information on how effectively a nucleotide probe selectively binds a target fragment in a target nucleotide sequence in a sample, comprising program code which, when executed, configures a computer to:
 (a) examine the target sequence for fragments capable of binding to the target fragment or the probe;   (b) generate equations to represent the binding reaction between the probe and the target fragment and the binding reactions identified in step (a); and   (c) solve the equations, for a lapsed time, to determine the concentration of the binding product between the probe and the target fragment.