Patent ID: 7711491
Filing Date: 2010-05-04
Classification: G16B

Abstract:
1. A method implemented by a computer system for computationally modeling DNA synthesis, the method comprising: in a bioinformatics module of the computer system: receiving a desired full-length DNA sequence and a length of starting oligos; using said desired full-length DNA sequence and a first pre-defined set of sequence-based rules to determine optimal starting oligos and well allocations of said optimal starting oligos capable of reducing the production of undesired product; and using a second pre-defined set of sequence-based rules to determine an optimal protocol for mixing the products of a first thermocycle into wells for subsequent thermocycles; in a thermodynamics module of the computer system: using said optimal starting oligos and well allocations determined in said bioinformatics module to track all possible reaction pathways that arise during each thermocycle and hybridization in terms of equilibrium thermodynamics by determining, for a given mix of DNA, the probability of hybridization for all the possible combinations of oligos as determined by the free energies of interaction, wherein the concentrations of all species of single and hybridized sequences in each well are determined as a function of processing conditions; extending all hybridized strands which can be biologically extended by the polymerase; and using all sequences and concentrations in a thermocycle as input for a subsequent thermocycle; in a kinetic module of the computer system, using said optimal starting oligos and well allocations determined in said bioinformatics module and said concentrations of all species determined in said thermodynamics module to track temporal and spatial evolution of hybridization and polymerization for all of said possible reaction pathways that arise during thermocycling and hybridization, by examining the probabilistic rate reaction of a particular reaction as a function of the probability rate for perfect matching attenuated by the probabilities based on the base-pair-specific thermodynamic free energies and oligomer proximities, relative orientations, mobilities and processing conditions; from an output module of the computer system: outputting predicted synthesis products information to a user based on outputs of said thermodynamic module and said kinetic module.