Biophysics of Artificially Expanded Genetic Information Systems. Thermodynamics of DNA Duplexes Containing Matches and Mismatches Involving 2-Amino-3-nitropyridin-6-one (Z) and Imidazo[1,2-a]-1,3,5-triazin-4(8H)one (P)

• DOI: 10.1021/acssynbio.6b00224
• Publication Date: 2017-01-18T00:50:06Z
• Authors: Xiaoyu Wang; Shuichi Hoshika; Raymond J. Peterson; Myong-Jung Kim; Steven A. Benner; Jason D. Kahn
• Keywords: 0303 health sciences; 03 medical and health sciences; Base Pair Mismatch; Pyridines; Biophysics; Oligonucleotides; Nucleic Acid Conformation; Nucleic Acid Hybridization; Thermodynamics; Hydrogen Bonding; Base Pairing

Synthetic nucleobases presenting non-Watson–Crick arrangements of hydrogen bond donor and acceptor groups can form additional nucleotide pairs that stabilize duplex DNA independent the standard A:T G:C pairs. The pair between 2-amino-3-nitropyridin-6-one 2′-deoxyriboside (presenting a {donor–donor–acceptor} bonding pattern on Watson–Crick face small component, trivially designated Z) imidazo[1,2-a]-1,3,5-triazin-4(8H)one an {acceptor–acceptor–donor} large P) is one these extra for which substantial amount molecular biology has been developed. Here, we report results UV absorbance melting measurements determine energetics binding strands containing Z P to give short duplexes Z:P as well various mismatches comprising P. All were done at 1 M NaCl in buffer (10 mM Na cacodylate, 0.5 EDTA, pH 7.0). Thermodynamic parameters (ΔH°, ΔS°, ΔG°37) oligonucleotide hybridization extracted. Consistent with model considers both geometric complementarity, was found contribute more stability than any involving either nonstandard nucleotide. Further, stable C:G pair. Z:G be most mismatch, forming deprotonated mismatched or wobble base analogous T:G mismatch. C:P less stable, perhaps observed C:O6-methyl-G, pyrimidine displaced into minor groove. Z:A T:P are much stable. Parameters predicting thermodynamics oligonucleotides bases provided. This represents first case where this synthetic genetic system.