title: Conformational aspects of an uncharged phosphate analogon built in at the branch-point of a DNA four-way junction.
abstract: Electrostatic interactions appear to be important in the conformation and dynamics of DNA four-way junctions. Particularly, the Coulomb repulsion between two approaching phosphate groups at the site of strand exchange is commonly supposed to have a negative influence on the thermodynamic stability of the fully stacked conformation. We synthesized a unimolecular DNA four-way junction containing an uncharged methylene-acetal linkage, -O3'-CH2-O5'-, instead of a regular phosphodiester linkage, -O3'-PO2-O5'-, between two specific residues at the branch-point to examine the effect of charge removal. Complete sequential 1H-NMR assignments of the non-exchangeable base protons and H1'/H2'/H2" sugar protons were obtained with the aid of NOESY and TOCSY experiments. On the basis of the NMR data it is concluded that the stacking arrangement at the branch-point of the modified oligonucleotide is similar to that of the previously studied parent four-way junction. Surprisingly, this is not the stacking arrangement in which the close phosphate-phosphate contact at the site of strand exchange would be absent. Some implications of this novel information regarding the role of the phosphate-phosphate repulsion in four-way junctions are discussed.
authors.affiliation: Leiden Institute of Chemistry Gorlaeus Laboratories, The Netherlands.
authors.forename: J A
authors.initials: JA
authors.lastname: Pikkemaat
authors.forename: F J
authors.initials: FJ
authors.lastname: Overmars
authors.forename: C M
authors.initials: CM
authors.lastname: Dreef-Tromp
authors.forename: H
authors.initials: H
authors.lastname: van den Elst
authors.forename: J H
authors.initials: JH
authors.lastname: van Boom
authors.forename: C
authors.initials: C
authors.lastname: Altona
mesh_terms: D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D010759:Phosphorus Isotopes; D011522:Protons; D014316:Tritium
chemical_list: D009841:Oligonucleotides; D010759:Phosphorus Isotopes; D011522:Protons; D014316:Tritium; D004247:DNA