Aptamers can be directly linked (conjugated) to drug conjugate or reporter molecules at any point of the sequence.
One of the most useful (and readily available) modifications of a wide variety of fluorophores. These can be added to either the 5’ or 3’ ends of the aptamer, or at any given point along its length.
Fluorescent aptamers also allow direct visualisation of the target, so they may be used as a more specific alternative to antibodies in techniques such as Western blotting. Aptamers would have many advantages in this sort of application, the most obvious of which is speed. As aptamers are highly specific for their target, they may be used directly after transfer to a membrane. They would negate the need for ‘membrane blocking,’ secondary antibodies or additional chemiluminescent reagents. As many fluorophores are available, multiple targets could be identified in a single sample
Aptamers may also be directly visualised in tissue samples or be used to follow binding and cellular localisation by confocal microscopy. The wide range of available fluorophores also means that multiple aptamers can be used in a single sample allowing co-localisation studies. Labelled aptamers may also be used for FACS analysis allowing identification of specific cell types or cellular markers within mixed cell production.
An extension of this is the conjugation of ‘FRET pairs’ or ‘fluorophore-quencher’ pairs to the selected aptamer. Target binding results in significant conformational change in the aptamer, which in turn changes the distance between the FRET pairs (or fluorophore and quencher) resulting in significant change in fluorescent output. This produces so called ‘aptamer beacons.’