A TT Dinucleotide with a Nonionic Silyl Backbone: Impact on Conformation and H-Bond Mediated Base Pairing as Studied by Low-Temperature NMR
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Eline M. Basílio Janke
Abstract
A TSiT dinucleotide linked through a nonionic diisopropylsilyl backbone has been synthesized and studied for its self-association through base–base recognition together with a free thymidine nucleoside. To characterize hydrogen-bonded associates in more detail, NMR measurements were performed in a freonic solvent at temperatures as low as 113 K in the slow hydrogen bond exchange regime. For the thymidine, TT base pairs with both the 2- and 4-carbonyl engaged in hydrogen bonds to the imino proton were observed. Whereas hydrogen bonds to the O4 acceptor are stronger as evidenced by a more deshielded proton in the hydrogen bridge when compared to hydrogen bonds to the O2 acceptor, the latter is nevertheless slightly favored over O4 in the H-bond formation of TT base pairs. The diisopropylsilyl linkage of the TSiT dinucleotide has no significant impact on the geometry and strength of formed NH–O2 and NH–O4 hydrogen bonds indicating, that the silyl backbone does not compromise the alignment of bases and does not pose any restrictions to the cyclic hydrogen bond formation between thymidines of the two strands. However, NMR results point to an exclusive formation of TSiT duplexes with an antiparallel strand orientation.
© by Oldenbourg Wissenschaftsverlag, München, Germany
Articles in the same Issue
- Editorial
- Biography of Prof. Dr. Hans-Heinrich Limbach
- Alumni and long term guests of the Limbach group
- NMR and FT-IR Studies on the Association of Derivatives of Thymidine, Adenosine, and 6-N-Methyl-Adenosine in Aprotic Solvents
- Competition between Hydrogen Bonds and Lewis Acid-Base Interactions in the Equilibria between Bis(pentafluorophenyl)borinic Acid and Pyridine: Insights from NMR, Diffractometric and Computational Studies
- Energy Analysis of Competing Non-Covalent Interaction in 1:1 and 1:2 Adducts of Collidine with Benzoic Acids by Means of X-Ray Diffraction
- A TT Dinucleotide with a Nonionic Silyl Backbone: Impact on Conformation and H-Bond Mediated Base Pairing as Studied by Low-Temperature NMR
- Oxygen and Hydrogen Isotopic Preference in Hydration Spheres of Chloride and Sulfate Ions
- Ab Initio Study of Cooperative Effects in Complexes X:HBO:Z, with X, Z=LiH, HNC, HF, HCN, HCl, ClF, and HBO: Structures, Binding Energies, and Spin-Spin Coupling Constants across Intermolecular Bonds
- The Structure and Dynamic Properties of 1H-Pyrazole-4-Carboxylic Acids in the Solid State
- Acridine – a Promising Fluorescence Probe of Non-Covalent Molecular Interactions
- First Example of Hydrogen Bonding to Platinum Hydride
- Interaction of Hydrogen with a Cobalt(0001) Surface
- Immobilization and Characterization of RuCl2(PPh3)3 Mesoporous Silica SBA-3
- Secondary Isotope Effects on 13C and 15N Chemical Shifts of Schiff Bases Revisited
- Analysis of Nutation Patterns in Fourier-Transform NMR of Non-Thermally Polarized Multispin Systems
- The Structure of Supercooled Water and the Mechanism of Homogeneous Nucleation of Ice Ih
- Probing Small Protonated Water Clusters in Acetonitrile Solutions by 1H NMR
- Double Hydrogen Transfer in Low Symmetry Porphycenes
- Nuclear Spin Selective Torsional States: Implications of Molecular Symmetry
Articles in the same Issue
- Editorial
- Biography of Prof. Dr. Hans-Heinrich Limbach
- Alumni and long term guests of the Limbach group
- NMR and FT-IR Studies on the Association of Derivatives of Thymidine, Adenosine, and 6-N-Methyl-Adenosine in Aprotic Solvents
- Competition between Hydrogen Bonds and Lewis Acid-Base Interactions in the Equilibria between Bis(pentafluorophenyl)borinic Acid and Pyridine: Insights from NMR, Diffractometric and Computational Studies
- Energy Analysis of Competing Non-Covalent Interaction in 1:1 and 1:2 Adducts of Collidine with Benzoic Acids by Means of X-Ray Diffraction
- A TT Dinucleotide with a Nonionic Silyl Backbone: Impact on Conformation and H-Bond Mediated Base Pairing as Studied by Low-Temperature NMR
- Oxygen and Hydrogen Isotopic Preference in Hydration Spheres of Chloride and Sulfate Ions
- Ab Initio Study of Cooperative Effects in Complexes X:HBO:Z, with X, Z=LiH, HNC, HF, HCN, HCl, ClF, and HBO: Structures, Binding Energies, and Spin-Spin Coupling Constants across Intermolecular Bonds
- The Structure and Dynamic Properties of 1H-Pyrazole-4-Carboxylic Acids in the Solid State
- Acridine – a Promising Fluorescence Probe of Non-Covalent Molecular Interactions
- First Example of Hydrogen Bonding to Platinum Hydride
- Interaction of Hydrogen with a Cobalt(0001) Surface
- Immobilization and Characterization of RuCl2(PPh3)3 Mesoporous Silica SBA-3
- Secondary Isotope Effects on 13C and 15N Chemical Shifts of Schiff Bases Revisited
- Analysis of Nutation Patterns in Fourier-Transform NMR of Non-Thermally Polarized Multispin Systems
- The Structure of Supercooled Water and the Mechanism of Homogeneous Nucleation of Ice Ih
- Probing Small Protonated Water Clusters in Acetonitrile Solutions by 1H NMR
- Double Hydrogen Transfer in Low Symmetry Porphycenes
- Nuclear Spin Selective Torsional States: Implications of Molecular Symmetry
