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Publication Abstract from PubMed

A crystal structure of a 108 nucleotide RNA-DNA complex containing a four-way junction was solved at 3.1 A resolution. The structure of the junction differs substantially from the "stacked-X" conformation observed previously, due to a 135 degrees rotation of the branches. Comparison of the two conformers provides insight into the factors contributing to the flexibility of four-way junctions. The stacked-X conformation maximizes base-stacking but causes unfavorable repulsion between phosphate groups, whereas the 135 degrees -rotated "crossed" conformation minimizes electrostatic clashes at the expense of reduced base-stacking. Despite the large rotation of the branches, both junction structures exhibit an antiparallel arrangement of the continuous strands and opposite polarity of the crossover strands.

Alternative conformations of a nucleic acid four-way junction.,Nowakowski J, Shim PJ, Stout CD, Joyce GF J Mol Biol. 2000 Jun 30;300(1):93-102. PMID:10864501^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.