Novel oligonucleotide analogues containing a morpholinoamidine unit

Morpholinoamidines were devised as new cationic units in oligonucleotides, by combining morpholino-nucleosides (to simplify the nomenclature, we will use the term morpholino-nucleosides to refer to nucleoside analogues in which the ribose ring was transformed into a morpholine) with internucleoside guanidines. Here, methodology was developed to synthesize oligonucleotides containing morpholinoamidines formed by morpholino-uridine and 5′-amino-5′-deoxythymidine. Morpholinoamidine was produced by solid-phase reaction of Alloc-morpholinocarbothioamide with 5′-aminonucleoside resin and Mukaiyamaʹs reagent activation. Two 14-mer oligonucleotides containing a single morpholinoamidine were synthesized and their affinity properties were investigated by forming DNA double and triple helices. Duplexes were slightly stabilized by a 3′ unit, but were less stable if internally positioned. Notably, triplexes were significantly stabilized at pH 7.0.