Thermal stability calculation of sticky ends
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Thermal stability calculation of sticky ends
Implementing the nearest-neighbor methods, the stability of sticky ends are revealed.
Basically, the nearest-neighbor method uses the sequence information for the calculation. The total free Gibbs of oligomers and melting temperature can be calculated from values of entropy, enthalpy, and concentration. Although different research groups have different results, all arrived at small difference between their calculation and empirical values: Santa et. al. (6.9%-8.9%), Naoki (2.2%-5.1%), etc.
Applying this nearest-neighbor method, DNAmazing provides accurate thermodynamic information of the short sticky ends.
The small difference of the results is attributed to the variety of the strand length and elementary values of each base pair propagation step, which comes from the calculation of the basis set of thermodynamics values. In order to have a detailed table of basis set of the propagation steps, various oligomers are tested their melting enthalpy, entropy with controlled composition and base-pair order.
Knowing the melting point and free Gibbs energy change of state will give us control over the binding/unbinding activities of the sticky ends with external binding sites.
