H-Phosphonate dA. dA(H-p)

H-phosphonate modification has a setup charge of $250.00 per order for special synthesis reagents .

Special notes on H-phosphonate modification.

1. H-phosphonate chimeric oligos. H-phosphonate bases/oligos can be synthesized in a sequence with standard bases or modifications containing phosphodiester linkages the 3' end of the sequence. If a chimeric oligo is designed then the H-phosphonate should be on the 5' end with no other standard phosphodiester bases at 5' of the H-phosphonate linked bases. Chemical oligo synthesis starts from the 3' and the phosphodiester linkages are generated by oxidation. Any such oxidation cycle after coupling the H-phosphonate will oxidize the H-phosphonate linkage to phosphodiester linkage.

2. Special oxidation. H-phosphonate modified oligos can be supplied with oligo bound to CPG solid support for the end user to perform special oxidation at the H-phosphonate linkage. Example is for S-35 radio-labeled phosphorothioate linkage. Please specify when placing an order.

H-phosphonoamidites are deoxynucleoside amidites modified such that, when incorporated into an oligonucleotide, that base position will have an H-phosphonate backbone linkage instead of the standard phosphodiester linkage. In the H-phosphonate linkage, one of the oxygen bound to the phosphorus atom in a phosphodiester linkage has been replaced by hydrogen. H-phosphonate-modified oligos are typically synthesized when a researcher wants to prepare a S-35 radiolabeled phosphorothioate linkage (1). For the radiolabeled phosphorothioate, an H-phosphonate linkage is incorporated at the desired position using phosphoramidite chemistry, and then S-35 is used to replace the hydrogen atom via a sulfurization reaction (2). For the phosphoroamidate, N,N-dimethylaminoethylamine is reacted with the H-phosphonate to form the substituted linkage. Phosphoroamidates, being a cationic linkage, may provide nuclease resistance and improved cell permeability (3).