CONFORMATIONAL ASPECTS OF AN UNCHARGED PHOSPHATE ANALOGON BUILT IN ATTHE BRANCH-POINT OF A DNA 4-WAY JUNCTION

Electrostatic interactions appear to be important in the conformation and dynamics of DNA four-way junctions. Particularly, the Coulomb repu lsion between two approaching phosphate groups at the site of strand e xchange is commonly supposed to have a negative influence on the therm odynamic 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 lin kage, -O3'-PO2--O5'-, between two specific residues at the branch-poin t to examine the effect of charge removal. Complete sequential H-1-NMR assignments of the non-exchangeable base protons and H1'/H2'/H2'' sug ar protons were obtained with the aid of NOESY and TOCSY experiments. On the basis of the NMR data it is concluded that the stacking arrange ment 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-ph osphate contact at the site of strand exchange would be absent. Some i mplications of this novel information regarding the role of the phosph ate-phosphate repulsion in four-way junctions are discussed. (C) 1996 Academic Press Limited