What factors affect hybridization?
• Assay Temperature which affects the equilibrium constant, hence the amount of binding. • Cation Concentration (K+, Na+, Mg++ etc. ) which affects the stability of one oligonucleotide binding to another. • Buffer Additives/Consistencies such as denaturants or viscosity. • Secondary Structure which affects any oligonucleotide and its ability to bind to another oligonucleotide or itself. • Synthetic nucleotide modification, such as Cy3 or Cy5 have the ability to increase or decrease binding. Q. How is secondary structure computed within the software? OMP Developer EditionTM uses a dynamic programming algorithm to calculate the energy of all possible structures by using our thermodynamic database. The optimal and nearby suboptimal structures are predicted to be most populated at equilibrium. Q. What is the nearest-neighbor model? Why is this important? The nearest-neighbor model uses empirical data to determine a set of “parameters” for all possible combinations of base pairs. By giving
