Precise Alkoxyamine Design to Enable Automated Tandem Mass Spectrometry Sequencing of Digital Poly(phosphodiester)s

A major step towards reliable reading of information coded in the sequence of long poly(phosphodiester)s was previously achieved by introducing an alkoxyamine spacer between information sub-segments. However, MS/MS decoding had to be performed manually to safely identify useful fragments of low abundance compared to side-products from the amide-based alkoxyamine used. Here, alternative alkoxyamines were designed to prevent side-reactions and enable automated MS/MS sequencing. Different styryl-TEMPO spacers were prepared to increase radical delocalization and stiffness of the structure. Their dissociation behavior was investigated by EPR and best results were obtained with spacers containing in-chain benzyl ring, with no side-reaction during synthesis or sequencing. Automated decoding of these polymers was performed using the MS-DECODER software, which interprets fragmentation data recorded for each sub-segment and re-align them in their original order based on location tags.

Automated summary

A novel alkoxyamine spacer was designed to prevent side-reactions and enable automated MS/MS sequencing of long poly(phosphodiester)s. Experimental results indicated that spacers containing in-chain benzyl ring showed the best performance, with no side-reactions during synthesis and excellent results during sequencing. The study also utilized MS-DECODER software for automated decoding of the polymers, interpreting fragmentation data and re-aligning them in their original order based on location tags.