Guiding the Design of Synthetic DNA-Binding Molecules with Massively Parallel Sequencing

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• 作者：Jordan L. Meier ; Abigail S. Yu ; Ian Korf ; David J. Segal ; Peter B. Dervan
• 刊名：The Journal of the American Chemical Society
• 出版年：2012
• 出版时间：October 24, 2012
• 年：2012
• 卷：134
• 期：42
• 页码：17814-17822
• 全文大小：639K
• 年卷期：v.134,no.42(October 24, 2012)
• ISSN：1520-5126

文摘

Genomic applications of DNA-binding molecules require an unbiased knowledge of their high affinity sites. We report the high-throughput analysis of pyrrole-imidazole polyamide DNA-binding specificity in a 10¹²-member DNA sequence library using affinity purification coupled with massively parallel sequencing. We find that even within this broad context, the canonical pairing rules are remarkably predictive of polyamide DNA-binding specificity. However, this approach also allows identification of unanticipated high affinity DNA-binding sites in the reverse orientation for polyamides containing 尾/Im pairs. These insights allow the redesign of hairpin polyamides with different turn units capable of distinguishing 5鈥?WCGCGW-3鈥?from 5鈥?WGCGCW-3鈥? Overall, this study displays the power of high-throughput methods to aid the optimal targeting of sequence-specific minor groove binding molecules, an essential underpinning for biological and nanotechnological applications.