title: Crystal structures of deprotonated nucleobases from an expanded DNA alphabet.
abstract: Reported here is the crystal structure of a heterocycle that implements a donor-donor-acceptor hydrogen-bonding pattern, as found in the Z component [6-amino-5-nitropyridin-2(1H)-one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine-pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely poly[[aqua(μ6-2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ido)sodium]-6-amino-5-nitropyridin-2(1H)-one-water (1/1/1)], denoted Z-Sod, {[Na(C5H4N3O3)(H2O)]·C5H5N3O3·H2O}n, and ammonium 2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ide-6-amino-5-nitropyridin-2(1H)-one-water (1/1/1), denoted Z-Am, NH4+·C5H4N3O3-·C5H5N3O3·H2O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.
authors.affiliation: Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Mariko F
authors.initials: MF
authors.lastname: Matsuura
authors.affiliation: Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA.
authors.forename: Hyo Joong
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Takahashi
authors.affiliation: Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Khalil A
authors.initials: KA
authors.lastname: Abboud
authors.affiliation: Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Benner
mesh_terms: D020029:Base Pairing; D019295:Computational Biology; D003460:Crystallization; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000138:chemical synthesis* / Q000737:chemistry; D006860:Hydrogen Bonding; D007202:Indicators and Reagents; D008958:Models, Molecular; D009711:Nucleotides / Q000737:chemistry*; D011522:Protons; D011743:Pyrimidines / Q000737:chemistry
chemical_list: D007202:Indicators and Reagents; D009711:Nucleotides; D011522:Protons; D011743:Pyrimidines; D003596:Cytosine; D004247:DNA
keywords: DNA alphabet; artificially expanded genetic information system (AEGIS); crystal structure; deprotonation; hydrogen bonds; pyrimidine nucleobase