Nucleobase Pairing in Expanded Watson-Crick-like Genetic Information Systems

Abstract

To guide the design of alternative genetic systems, we measured melting temperatures of DNA duplexes containing matched and mismatched nucleobase pairs from natural and unnatural structures. The pairs were analyzed in terms of structural features, including nucleobase size, number of hydrogen bonds formed, the presence of uncompensated hydrogen bonding functional groups, the nature of the bond joining the nucleobase to the sugar, and nucleobase charge. The results suggest that stability of nucleobase pairs correlates with the number of H-bonds, size complementarity, the presence of uncompensated functional groups, and the presence of charge on a nucleobase. Each of these properties appear to be more significant than the nature of the glycosidic bond and sequence context. The results provide guidelines for constructing stable Watson-Crick like nucleobase pairs with unnatural nucleobases. The experiments also demonstrate that expanded genetic systems can be constructed using size complementary nucleobase pairs that contain three hydrogen bonds.

Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs Are Replaced by isoG−isoC Pairs

“…[13][14][15][17][18][19] The Watson-Crick like iGiC pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet [20][21][22][23][24][25][26] for further understanding interactions that shape nucleic acid structure (Figure 1). 7,[25][26][27][28][29][30][31][32] Here, thermodynamic studies of tandem GA pairs flanked by iGiC pairs are reported along with NMR structures of the RNA duplexes (GCiGGAiCGCA) 2 and (GGiCGAiGCCA) 2 . NMR restrained molecular dynamics and energy minimization of (GCiGGAiCGCA) 2 reveal a conformation of tandem sheared GA pairs closed by Watson-Crick like iGiC pairs.…”

Primitive Genetic Polymers

“…The successful incorporation of nonnatural base pairs into nucleic acid duplexes has given ample reason to seriously consider this question (Switzer et al 1989;Piccirilli et al 1990;Geyer et al 2003). Most of the nonnatural base pairs studied thus far have maintained the form of a base comprised of a six-membered ring (like a pyrimidine) paired with a base comprised of fused five-and six-membered rings (like a purine), which can be accommodated in a helix also containing canonical WatsonCrick base pairs.…”

Directed Evolution of Polymerases To Accept Nucleotides with Nonstandard Hydrogen Bond Patterns

“…1−11 Our laboratories have constructed an artificially expanded genetic information system (AEGIS). 10,12 The AEGIS is a species of DNA having additional nucleobases that present alternative hydrogen bonding patterns, allowing its members to form mutually exclusive pairing schemes. Some members of the AEGIS are used in the clinic to monitor the viral load of patients infected with human immunodeficiency virus and hepatitis C virus.…”