# Efficiency of Digital Photolithographic Synthesis of Large, High-Quality DNA Libraries and Microarrays using a Guanine O6 Dephosphitylation Strategy

## TL;DR

This paper introduces a new method to improve DNA microarray synthesis by reducing errors caused by guanine O6-phosphitylation.

## Contribution

The novel debranching step using standard capping reagents suppresses depurination-based fragmentation during DNA synthesis.

## Key findings

- A short debranching step significantly reduces oligonucleotide fragmentation during synthesis.
- The method enhances the synthetic yield of large DNA libraries and microarrays.
- Digital maskless photolithography is effectively combined with the debranching strategy.

## Abstract

Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA, RNA, synthetic nucleic acid analogs, non-nucleosidic building blocks, or combinations of these. Large oligonucleotide libraries are synthesized as microarrays and used in situ for surface-based assays or cleaved for off-array applications. Here, using a digital maskless photolithographic approach, we address an important source of error in DNA microarray synthesis, oligonucleotide fragmentation arising from the O6-phosphitylation of guanine during the potentially hundreds of coupling cycles required for complex library synthesis. Introducing a very short debranching step using standard capping reagents suppresses depurination-based fragmentation and greatly enhances synthetic yield.

Large-scale de novo nucleic acid synthesis is crucial for advancing genomics, therapeutics, and synthetic biology, yet errors in DNA microarray synthesis hinder progress. Here, the authors employ a digital maskless photolithographic approach, introducing a debranching step to reduce depurination-based fragmentation arising from the O6-phosphitylation of guanine and improve synthetic yield.