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Pyrrole-imidazole polyamides : manual solid-phase synthesis

Pauff, Steven M. and Fallows, Andrew J. and Mackay, Simon P. and Su, Wu and Cullis, Paul M. and Burley, Glenn A. (2015) Pyrrole-imidazole polyamides : manual solid-phase synthesis. In: Current Protocols in Nucleic Acid Chemistry. Wiley, [S.I.]. ISBN 9780471142706

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Pyrrole-imidazole polyamides (PAs) are a family of DNA-binding peptides that bind in the minor groove of double-stranded DNA (dsDNA) in a sequence-selective, programmable fashion. This protocol describes a detailed manual procedure for the solid-phase synthesis of this family of compounds. The protocol entails solution-phase synthesis of the Boc-protected pyrrole (Py) and imidazole (Im) carboxylic acid building blocks. This unit also describes the importance of choosing the appropriate condensing agent to form the amide linkages between each building block. Finally, a monomeric coupling protocol and a fragment-based approach are described that delivers PAs in 13% to 30% yield in 8 days.