Controlling Glycosyl Bond Conformation of Guanine Nucleosides: Stabilization of the anti Conformer in 5'-O-Ethylguanosine

Structural Characterization of 6-Thioguanosine and Its Monohydrate in the Gas Phase

Detailed structural analysis of 6-thioguanosine (6TGs) in relation to its tautomerization and sugar conformation is performed in the gas phase using UV and IR spectroscopy combined with ab initio calculations. We have observed a thiol tautomer of 6TGs with its sugar moiety in the syn conformation that is stabilized by a strong intramolecular H-bonding between O5'H of the sugar and N3 atom of the guanine moiety. This observation is consistent with previous results for guanosine (Gs) in which the corresponding enol form is solely detected. We have also identified a monohydrate of 6TGs consisting of a thiol tautomer with the water linking guanine moiety and sugar OH group. It is demonstrated that hydration behavior of 6TGs is significantly different from that of Gs as a result of a weaker H-bonding ability of the thiol group.

The Research of G-Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes

A detailed understanding of the mismatched base-pairing interactions in DNA will help reveal genetic diseases and provide a theoretical basis for the development of targeted drugs. Here, we utilized mononucleotide fragment to simulate mismatch DNA interactions in a local hydrophobic microenvironment. The bipyridyl-type bridging ligands were employed as a mild stabilizer to stabilize the GG mismatch containing complexes, allowing mismatch to be visualized based on X-ray crystallography. Five single crystals of 2′-deoxyguanosine–5′–monophosphate (dGMP) metal complexes were designed and obtained via the process of self-assembly. Crystallographic studies clearly reveal the details of the supramolecular interaction between mononucleotides and guest intercalators. A novel guanine–guanine base mismatch pattern with unusual (high anti)–(high anti) type of arrangement around the glycosidic angle conformations was successfully constructed. The solution state ¹H–NMR, ESI–MS spectrum studies, and UV titration experiments emphasize the robustness of this g–motif in solution. Additionally, we combined the methods of single-crystal and solution-, solid-state CD spectrum together to discuss the chirality of the complexes. The complexes containing the g–motif structure, which reduces the energy of the system, following the solid-state CD signals, generally move in the long-wave direction. These results provided a new mismatched base pairing, that is g–motif. The interaction mode and full characterizations of g–motif will contribute to the study of the mismatched DNA interaction.

Gas-phase hydration of the lysozyme ion produced by infrared-laser ablation of a droplet beam studied by photodissociation and fluorescence spectroscopy

Biomolecules function in an aqueous environment. Elucidation of the hydration structures of biomolecules is hence important to understand their functions. Here, we investigated the hydration structure of lysozyme (Lys) in the gas phase by photodissociation and fluorescence spectroscopy in combination with droplet-beam laser ablation mass spectrometry. We found that water molecules are held inside and on the surface of the Lys molecule, and the hydration structure around the tryptophan residue changes by photoexcitation. This study provides a novel method to observe the hydration structures of large biomolecules at the molecular level.

Modulation of Conformational Preferences of Heteroaromatic Ethers and Amides through Protonation and Ionization: Charge Effect

Multiple approaches reveal the strong effects of a positive charge introduced by protonation or ionization on the conformation of o‐heteroaromatic ethers and amides. The ethers and amides containing an ortho‐N heteroatom are syn‐preferring while those containing an ortho‐O or ortho‐S heteroatom are mostly anti‐preferring. However, for all the monocyclic o‐heteroaromatic ethers and amides, the protonated ones are all anti‐preferring while the ionized ones are all syn‐preferring. Interestingly, although both the protonation and ionization introduce a positive charge, they have such different effects on molecular conformation, very informative for understanding the origin of conformational preferences. Detailed analysis shows that the population of the introduced positive charge dictates the conformational preferences via electrostatic and orbital interactions. Compared to ortho‐heteroatoms, meta‐heteroatoms have weaker effect on conformational preference. Achieved by complete inductive method, the regularity of conformational preferences and switching provides easy ways to modulate conformers (by pH or redox), and makes this kind of ether or amide bond a conformational hinge applicable to design of functional molecules (drugs and materials) and modulation of molecular biological processes.

Reactions of water with radical cations of guanine, 9-methylguanine, 2′-deoxyguanosine and guanosine: keto–enol isomerization, C8-hydroxylation, and effects of N9-substitution

The reactions of D₂O with guanine radical cations in nucleobases and nucleosides were studied in the gas phase using the guided-ion-beam experiment and computational modeling.

How nature covers its bases

The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.

Gas-Phase IR Spectroscopy of Nucleobases

IR spectroscopy of nucleobases in the gas phase reflects simultaneous advances in both experimental and computational techniques. Important properties, such as excited state dynamics, depend in subtle ways on structure variations, which can be followed by their infrared signatures. Isomer specific spectroscopy is a particularly powerful tool for studying the effects of nucleobase tautomeric form and base pair hydrogen-bonding patterns.

Gas-phase structure and reactivity of the keto tautomer of the deoxyguanosine radical cation

Gas-phase IR spectroscopy, ion–molecule reactions, collision-induced dissociation and computational chemistry in combination form a powerful tool to gain insights into the structure of one-electron oxidised guanine in DNA and its resultant chemistry.

Solvation effect on the NH stretching vibrations of solvated aminopyrazine, 2-aminopyridine, and 3-aminopyridine clusters

The vibrational spectra of the hydrated and methanol-solvated aminopyrazine, 2-aminopyridine and 3-aminopyridine in supersonic jets have been measured in terms of IR-UV double-resonance spectroscopy. Comparing the IR spectrum of aminopyrazine with those of 2-aminopyridine and 3-aminopyridine clusters, we determine the solvation structure of aminopyrazine to be a similar cyclic structure as hydrated 2-aminopyridine clusters [Wu, et al., Phys. Chem. Chem. Phys. 2004, 6, 515]. In the case of monohydrated aminopyrazine cluster, one of the normal modes composed of the hydrogen-bonded OH and NH stretching local modes gives the anomalously weak IR intensity, which is ascribed to the cancellation of the dipole moment change between the OH and NH stretching local modes. The solvated 3-aminopyridine clusters forms the hydrogen-bond between the pyridyl nitrogen atom and the OH group, but the amino group is indirectly affected to induce slight blue shift of the NH(2) stretches. This phenomenon is explained by inductive effect where the electron withdrawing from the amino group upon the solvation results in a "quinoid-like" structure of the amino group.