Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides.

@article{Nakano2009DynamicsAE,
  title={Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides.},
  author={Shu-Ichi Nakano and Hirohito Oka and Yuuki Uotani and Kazuya Uenishi and Masayuki Fujii and Naoki Sugimoto},
  journal={Biochemistry},
  year={2009},
  volume={48 47},
  pages={
          11304-11
        }
}
A base flipping conformation is found in many biological processes, including DNA repair and DNA and RNA modification processes. To investigate the dynamics and energetics of this unusual conformation in a double helix, base flipping induced by the base pair analogues of deoxyadenosine and deoxycytidine derivatives tethering a phenyl or naphthyl group was investigated. DNA strands bearing the base pair analogues stabilized the base flipping conformation of a complementary RNA, resulting in a… Expand
Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides.
TLDR
The thermal stability of DNA duplexes containing a non-natural nucleotide tethered to a simple aromatic hydrocarbon group devoid of dipole moments and hydrogen bonding sites was measured to understand nucleic acid interactions and to design new non- natural nucleotides. Expand
Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules
TLDR
It is suggested that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. Expand
Base-pairing selectivity of a ureido-linked phenyl-2'-deoxycytidine derivative.
TLDR
Insight into the pairing selectivity of carbamoylated cytosine lesions produced in cells is provided, and applications of the 2'-deoxycytidine derivatives in medical technologies, molecular biology experiments, and synthesis of a supramolecular network of DNA strands are suggested. Expand
Hydration changes upon DNA folding studied by osmotic stress experiments.
TLDR
The thermodynamic stability of DNA oligonucleotide structures in the presence of high background concentrations of neutral cosolutes is described to suggest that the sugar-phosphate backbone and the integrity of the basepair conformation make important contributions to the binding of water molecules to the DNA bases and helical grooves. Expand
Dual base-flipping of cytosines in a CpG dinucleotide sequence.
TLDR
The results presented in this paper suggest that the extra-helical conformation of the methyl-cytosine recognized by UHRF1 can facilitate the base-flipping process of the target cytosine to be methylated by Dnmt1. Expand
Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions
TLDR
Nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions are summarized. Expand
Base-flipping propensities of unmethylated, hemimethylated, and fully methylated CpG sites.
TLDR
Results from molecular dynamics simulations indicating that methylation of CpG sites suppresses spontaneous extra-helical conformations of either of the two cytosines are presented, conjecture that the mechanism for base flipping observed in complexes between hemimethylated DNAs and proteins is not likely to be passive. Expand
New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics.
TLDR
Each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface, and rings of all NABs become almost equally flexible in the dynamic aqueous environment. Expand
Use of a Ureido-Substituted Deoxycytidine Module for DNA Assemblies
TLDR
An N-phenylcarbamoyl deoxycytidine nucleoside was incorporated into a C-rich oligonucleotide to achieve self-assembly in aqueous solution and the capability of the module to form DNA assemblies varied depending on the number of modules incorporated. Expand
Quantum chemical study of the equatorial/axial exchange of different substituents in nitrogen and phosphorous-containing 6-membered rings: Role of charge transfer interactions
Understanding the nature of equatorial/axial conversion in six-membered rings is important because of involvement of these motifs in some biological systems. In this work we have studied theExpand
...
1
2
...