Discovery, Characterization, and Optimization of an Unnatural Base Pair for Expansion of the Genetic Alphabet

Aaron M. Leconte, Gil Tae Hwang, Shigeo Matsuda, Petr Capek, Yoshiyuki Hari, and Floyd E. Romesberg*
Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037
J. Am. Chem. Soc., 2008, 130 (7), pp 2336–2343
DOI: 10.1021/ja078223d
Publication Date (Web): January 25, 2008
Copyright © 2008 American Chemical Society
*

In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.

, floyd@scripps.edu

Abstract

Abstract Image

DNA is inherently limited by its four natural nucleotides. Efforts to expand the genetic alphabet, by addition of an unnatural base pair, promise to expand the biotechnological applications available for DNA as well as to be an essential first step toward expansion of the genetic code. We have conducted two independent screens of hydrophobic unnatural nucleotides to identify novel candidate base pairs that are well recognized by a natural DNA polymerase. From a pool of 3600 candidate base pairs, both screens identified the same base pair, dSICS:dMMO2, which we report here. Using a series of related analogues, we performed a detailed structure−activity relationship analysis, which allowed us to identify the essential functional groups on each nucleobase. From the results of these studies, we designed an optimized base pair, d5SICS:dMMO2, which is efficiently and selectively synthesized by Kf within the context of natural DNA.

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History

  • Published In Issue February 20, 2008
  • Received October 26, 2007

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