Several products may be used to investigate the effect on the activity of an oligonucleotide when key structural elements are changed. The 7-deaza purine monomers lack groups critical for hydrogen bonding. 7-Deaza-8-aza-A and 7-deaza-8-aza-G (PPG) monomers are isomers of A and G and have similar electron density. Their presence in oligos is slightly stabilizing relative to A and G. Unlike G, PPG does not lead to aggregation and G-rich oligos can be easily prepared and isolated. 5'-Fluorescein oligos with PPG at the 5'-terminus are much less quenched than the equivalent G oligos. As a purine analogue of Thymidine, 7-deaza-2'-deoxyXanthosine (7-deaza-dX) promises to have interesting effects on DNA structure of triplexes. 7-Deaza-dX also forms a non-standard base pair with a 2,4-diaminopyrimidine nucleoside analogue. Standard nucleobases have an unshared pair of electrons that project into the minor groove of duplex DNA. Enzymes that interact with DNA, polymerases, reverse transcriptases, restriction enzymes, etc., may use a hydrogen bond donating group to contact the hydrogen bond acceptor in the minor groove. 3-Deaza-2'-deoxyadenosine is very interesting in that it maintains the ability for regular Watson-Crick hydrogen bonding to T but is lacking the electron pair at the 3-position normally provided by N3.
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.
Psoralen C2 is designed to crosslink to a T residue adjacent to the 3'-terminus of the opposite strand of double stranded DNA. Psoralen C6 is intended to fulfill the same purpose but, with the longer spacer, crosslinks to the triple strand of triplex DNA.Max excitation=330nm, observed at max 395nm||