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. Author manuscript; available in PMC: 2011 Jul 1.
Published in final edited form as: Methods. 2010 Feb 21;51(3):347–357. doi: 10.1016/j.ymeth.2010.02.017

TABLE 3.

Calculations

% Fully Synthesized Product : {(b)/(b+c+a)} * 100
Where, “b” is the fully synthesized product, “c” are the intermediate synthesis products and “a” is the remaining unsynthesized substrate.
% Cleaved Product : {(b)/(b+a)} * 100
Where, “b” is the cleaved product and “a” is the remaining
uncleaved substrate.
% Ligated Product: {(b)/(b+a)} * 100
Where, “b” is the ligated product and “a” is the remaining unligated substrate.
% Bound Product: {(b)/(b+a)} * 100
Where, “b” is the bound product and “a” is the remaining unbound substrate.
% Unwound Product: {(b)/(b+a)} * 100
Where, “b” is the unwound product and “a” is the remaining unwound substrate
Strand Melting is measured in a similar manner.
% Annealed Product: {(b)/(b+a)} * 100
Where, “b” is the annealed product and “a” is the remaining unannealed substrate
Calculation of Dissociation Constants: After EMSA, the curves are fit using nonlinear least square regression of
the hyperbolic equation:
y = Bmax*[Protein]/(Kd + [Protein])
where, y is the percent of the oligonucleotide bound, [Protein] is the concentration of protein in nM, Bmax is the maximum
binding and Kd is the equilibrium dissociation constant.