Patent ID: 11915794
Assignee: CHAKRABARTI ADVANCED TECHNOLOGY LLC
Field: Computer technology (Electrical engineering)
Classification: CPC G  C | IPC C  G

Claim 4:
5. A system for enhancing annealing efficiency of first and second single strands of deoxyribonucleic acid (DNA) in a polymerase chain reaction (PCR) cycle at a predetermined time, the method comprising:
an amplification apparatus;
a memory device; and
a processor coupled to the memory device, the processor configured to:
(a) receive information comprising sequences of single strand DNA and primer, concentrations of the single strand DNA and primer, length of a predetermined time period for annealing the single strand DNA and primer and a set of annealing reaction temperatures;
(b) determine the forward reaction rate constant, kf, of annealing the single strand DNA and primer at annealing reaction temperatures in the set;
(c) determine the reverse reaction rate reaction rate constant, kr, of annealing the single strand DNA and primer at reaction temperatures in the set; and
(d) select one or more of the annealing reaction temperatures sufficient to produce a primer hybridized DNA strand concentration in excess of a predetermined threshold within the predetermined time period for annealing; and
at least one output interface for communicating the one or more annealing reaction temperatures to the amplification apparatus, wherein the amplification apparatus conducts the annealing to produce the primer hybridized DNA strand concentration in excess of the predetermined threshold within the predetermined time period,
wherein the hybridized DNA strand concentration, [SP], is determined according to:

d[SP]/dt=kf[S][P]−kr[SP]

wherein [P] is concentration of the primer and [S] is concentration of the single strand DNA; and
wherein kf and kr are calculated according to Gibbs free energy for the annealing reaction and relaxation time for the annealing reaction, and wherein relationship between the Gibbs free energy, kf and kr is expressed as:, k
    f
   
   
    k
    r
   
  
  =
  
   
    [
    
     C
     o
    
    ]
   
   ⁢
   
    exp
    ⁡
    (
    
     
      
       -
       Δ
      
      ⁢
      G
     
     
      R
      ⁢
      T
     
    
    )
   
  
 

wherein [C0] is the standard concentration, R is the gas constant and T is the annealing reaction temperature and the relaxation time τ is expressed as:

τ=1/(kf[Peq+Seq]+kr)

wherein Peq and Seq are equilibrium concentrations of the primer and single strand DNA.