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Simone Budow

Publications and source records attributed to Simone Budow.

6 recordsLinked to original sources
PubMed2006

2'-Deoxy-5-propynylcytidine: a nucleoside forming two solid-state conformations.

The title compound, 4-amino-1-(2-deoxy-beta-D-erythropentofuranosyl)-5-(prop-1-ynyl)pyrimidin-2(1H)-one, C12H15N3O4, shows two conformations in the crystalline state which differ mainly in the glycosylic bond torsion angle and the sugar pucker. Both molecules exhibit an anti glycosylic bond conformation, with torsion angles chi = -135.0 (2) and -156.4 (2) degrees for molecules 1 and 2, respectively. The sugar moieties show a twisted C2'-endo sugar pucker (S-type), with P = 173.3 and 192.5 degrees for molecules 1 and 2, respectively. The crystal structure is characterized by a three-dimensional network that is stabilized by several intermolecular hydrogen bonds between the two conformers.

Crystallography, X-Ray↗
PubMed2006

2'-Deoxy-7-propynyl-7-deazaadenosine: a DNA duplex-stabilizing nucleoside.

In the title compound, 2'-deoxy-7-propynyl-7-deazaadenosine, C14H16N4O3, the torsion angle of the N-glycosylic bond is anti [chi = -130.7 (2) degrees ]. The sugar pucker of the 2'-deoxyribofuranosyl moiety is C2'-endo-C3'-exo, 2T3 (S-type), with P = 185.9 (2) degrees and tau(m) = 39.1 (1) degrees , and the orientation of the exocyclic C4'-C5' bond is -ap (trans). The 7-substituted propynyl group is nearly coplanar with the heterocyclic base moiety. Molecules of the nucleoside form a layered network in which the heterocyclic bases are stacked head-to-tail with a closest distance of 3.197 (1) A. The crystal structure of the nucleoside is stabilized by three intermolecular hydrogen bonds of types N-H... O, O-H... N and O-H... O.

Crystallography, X-Ray↗
PubMed2006

N8-(2'-O-methylribofuranosyl)-8-aza-7-deazaadenine monohydrate.

In the title compound, 4-amino-2-(2-O-methyl-beta-D-ribofuranosyl)-2H-pyrazolo[3,4-d]pyrimidine monohydrate, C11H15N5O4.H2O, the conformation of the N-glycosylic bond is syn [chi = 20.1 (2) degrees ]. The ribofuranose moiety shows a C3'-endo (3T2) sugar puckering (N-type sugar), and the conformation at the exocyclic C4'-C5' bond is -ap (trans). The nucleobases are stacked head-to-head. The three-dimensional packing of the crystal structure is stabilized by hydrogen bonds between the 2'-O-methylribonucleosides and the solvent molecules.

Adenine↗
PubMed2005

Stabilization of tandem dG-dA base pairs in DNA-hairpins: replacement of the canonical bases by 7-deaza-7-propynylpurines.

The stabilizing effect of 7-propynylated 7-deazapurine nucleosides on DNA-hairpins and DNA-duplexes containing d(GA) mismatches was investigated. The corresponding oligonucleotides were synthesized using solid-phase synthesis. For this purpose, the phosphoramidite of 7-deaza-7-propynyl-2'-deoxyadenosine (3c) was prepared. The incorporation of 3c instead of dA into the tandem d(GA) base pair of a DNA-hairpin alters the secondary structure, but has a positive effect on the duplex stability. A complete replacement of the canonical nucleosides of the tandem d(GA) base pair by 3c and 7-deaza-7-propynyl-2'-deoxyguanosine results in a significant base pair stabilization.

Base Pairing↗
PubMed2005

8-Aza-7-deaza-2'-deoxy-2-(methylsulfanyl)adenosine.

In the title compound, 4-amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-6-methylsulfanyl-1H-pyrazolo[3,4-d]pyrimidine, C11H16N5O3S, the conformation of the glycosidic bond is between anti and high anti. The 2'-deoxyribofuranosyl moiety adopts the C3'-exo-C4'-endo conformation (3T4, S-type sugar pucker), and the conformation at the exocyclic C-C bond is +sc (+gauche). The exocyclic 6-amine group and the 2-methylsulfanyl group lie on different sides of the heterocyclic ring system. The molecules form a three-dimensional hydrogen-bonded network that is stabilized by O-H...N, N-H...O and C-H...O hydrogen bonds.

Adenosine↗