The answer is complicated because there are many ways to place different conjugations on an oligonucleotide, but we are limited by what is available for conjugation and by compatibility issues. The easiest way is if one or both of the conjugates are available as a phosphoramidite and/or support bound reagents. If at least one reagent is available, the other conjugate can often be attached through a primary amine at the other end of the oligonucleotide. Chemical compatibility is avoided in this case. If neither conjugate is available as a phosphoramidite or support bound reagent, then we often will use an orthogonal linker scheme incorporating both a thiol linker and an amino linker. This requires that one of the conjugates is available as a maleimide, which is thiol specific under neutral pH conditions. Most of all the commonly used dyes are available in both the succinimidyl and maleimidyl ester forms. The most common, such as fluorescein, TET, HEX, TAMRA, Cyanine 5 and Cyanine 3 are also available as phosphoramidites or support bound reagents. We will help you design your specific oligonucleotide when you place your order.