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Base flipping induced by the base pair analogues of deoxyadenosine and deoxycytidine derivatives tethering a phenyl or naphthyl group was explored to study the dynamics and energetics of unusual conformation observed during DNA repair and DNA and RNA modification processes. The results for the base flipping which occurred in competition with base pair formation could be applied to study the base flipping conformation under the equilibrium with base pairing.

Ureido-substituted cytosine derivatives are promising for constructing self-assembly structures that can be applied to nanotechnology research. However, conventional cytosine modules achieve assembly in organic solvents. In this study, an N-phenylcarbamoyl deoxycytidine nucleoside was incorporated into a C-rich oligonucleotide to achieve self-assembly in aqueous solution. The results show that the capability of the module to form DNA assemblies varied depending on the number of modules incorporated. The deoxycytidine derivative has a potential application in the development of smart materials based on DNA assembly. [ABSTRACT FROM PUBLISHER]

Incorporation of modified nucleotides into nucleic acid strands often produces conformational constraints and steric hindrances that may change the property of base pairing. In this study, we investigated a 2'-deoxycytidine derivative that tethers a phenyl moiety to the exocyclic amino group of cytosine linked through a ureido group. This derivative compound is structurally similar to the carbamoylated DNA base lesions produced in cells. The thermodynamic and structural studies showed that the modified dC formed the base pair with dG in the complementary strand, but the base-pairing selectivity toward dG was decreased under poly(ethylene glycol)-mediated osmotic stress. The phenyl group and the ureido linker attached to dC provided selectivity for the formation of base pairing exclusively with dG in a wide range of pH conditions, whereas unmodified dC stabilized the pairings with dA or dC in acidic solutions. Moreover, this modified base could not form self-pairing through intermolecular hydrogen bonds. We suggest that formation of weak pairing and protonation of the cytosine base are hindered due to the base modification. These data provide insights into the pairing selectivity of carbamoylated cytosine lesions produced in cells, and suggest applications of the 2'-deoxycytidine derivatives in medical technologies, molecular biology experiments, and synthesis of a supramolecular network of DNA strands.

Water-soluble neutral cosolutes can be used to quantify biomolecular properties in the particular molecular environment occurring in a cell. We studied the conformation and the thermal stability of DNA and RNA structures in the presence of PEG [poly(ethylene glycol)] and smaller cosolutes of glycerol, ethylene glycol, 1,3-propanediol, 2-methoxyethanol, and 1,2-dimethoxyethane. Although the neutral cosolutes destabilized the oligonucleotide duplex and the hairpin structures, the left-handed Z-form duplex was more energetically favored in the cosolute-containing solutions. These observations were due to the contribution of water molecule on the nucleotide structure formations because the cosolutes act as an osmolyte to reduce the water activity of a solution. Moreover, the sodium ion condensation for the duplex and the hairpin formations was reduced in the presence of PEG, while that for the transition from the B-form to the Z-form was unaltered. The CD (circular dichroism) and EPR (electron paramagnetic resonance) spectra demonstrated that the cosolutes changed the helical conformation of the unstructured oligonucleotides, but not those of the ordered structures. The results of the favorable formation of the noncanonical nucleotide structures, and minimized conformational and thermal perturbations of the ordered nucleotide structures in the cosolute-containing solutions implicate the significance of the intracellular environment on DNA and RNA structures in a cell.

We developed the base pair-mimic nucleosides tethering the phenyl group and the naphtyl group, synthesized from deoxyadenosine (Aphe and Anaph) and deoxycytidine (Cphe and Cnaph). Structure and the thermal stability of the DNA duplexes containing the deoxyadenosine derivatives or the deoxycytidine ones in the middle of a DNA strand were obtained by the CD spectra and the UV melting curves. The DeltaGo37 values among DNA duplexes containing Aphe-A, Aphe-G, Aphe-C and Aphe-T pair differed only by 1.9 kcal mol(-1). The DNA duplexes containing Cphe also showed the DeltaGo37 values differed by 1.0 kcal mol-1 despite opposite base nucleotide, except the duplex containing the Cphe-G pair. Interestingly, the duplex consisting of the DNA containing the base pair-mimic nucleosides and the complementary RNA strand caused the site-selective RNA hydrolysis except the Cphe-G pair. This data suggests that the Cphe has an ability of forming the base pair with guanosine.

We previously reported that the deoxyadenosine derivative tethering the phenyl group at the N6 position of deoxyadenosine, A(phe) stacked efficiently with the adjacent nucleotide bases at a DNA duplex terminus and in the middle of a DNA duplex. In contrast with the observations for A(phe), this study revealed that the phenyl group of the deoxycytidine derivative, C(phe) located outside the helix and allowed the base pair formation with guanine in a DNA duplex, although its phenyl group could stack with the adjacent DNA bases as efficient as A(phe). Klenow fragment of DNA polymerase I and T7 DNA polymerase selectively incorporated dTTP and dGTP opposite A(phe) and C(phe) in the template DNA, respectively, implying that the conformation of A(phe) differs between in the DNA polymerase and in solution.