Nucleic Acids Research Advance Access originally published online on October 29, 2006
Nucleic Acids Research 2006 34(21):6095-6101; doi:10.1093/nar/gkl633
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Nucleic Acids Research, 2006, Vol. 34, No. 21 6095-6101
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Chemistry |
Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Foundation for Applied Molecular Evolution 1115 NW 4th Street, Gainesville, FL 32601, USA
*To whom correspondence should be addressed at Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville FL 32604-1174, USA. Tel: +1 352 271 7005; Fax: +1 352 271 7076; Email: sbenner{at}ffame.org
Received June 14, 2006. Revised August 9, 2006. Accepted August 12, 2006.
To support efforts to develop a ‘synthetic biology’ based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1'-ß-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson–Crick complement, the purine analog 2-amino-8-(1'-ß-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where ‘py’ indicates a pyrimidine analog and ‘pu’ indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA.
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