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Full-Text Articles in Physical Sciences and Mathematics
Relative Stabilities Of Dna 3-Way, 4-Way And 5-Way Junctions (Multi-Helix Junction Loops) - Unpaired Nucleotides Can Be Stabilizing Or Destabilizing, Neocles B. Leontis, Julie L. Kardmas, Amy J. Ravin
Relative Stabilities Of Dna 3-Way, 4-Way And 5-Way Junctions (Multi-Helix Junction Loops) - Unpaired Nucleotides Can Be Stabilizing Or Destabilizing, Neocles B. Leontis, Julie L. Kardmas, Amy J. Ravin
Chemistry Faculty Publications
Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits the assembly of five-way DNA junction complexes (5WJ) having as few as seven basepairs per arm from five mutually complementary oligonucleotides. Previous work showed that 5WJ, having eight basepairs per arm but lacking unpaired bases, could not be assembled I[Wang,Y.L., Mueller,J.E., Kemper,B. and Seeman,N.C. (1991) Biochemistry, 30, 5667-5674]. Competition binding experiments demonstrate that four-way junctions (4WJ) …
Stability And Structure Of Three-Way Dna Junctions Containing Unpaired Nucleotides, Neocles B. Leontis, Wendy Kwok, Jennifer S. Newman
Stability And Structure Of Three-Way Dna Junctions Containing Unpaired Nucleotides, Neocles B. Leontis, Wendy Kwok, Jennifer S. Newman
Chemistry Faculty Publications
Non-paired nucleotides stabilize the formation of three-way helical DNA junctions. Two or more unpaired nucleotides located in the junction region enable oligomers ten to fifteen nucleotides long to assemble, forming conformationally homogeneous junctions, as judged by native gel electrophoresis. The unpaired bases can be present on the same strand or on two different strands. Up to five extra bases on one strand have been tested and found to produced stable junctions. The formation of stable structures is favoured by the presence of a divalent cation such as magnesium and by high monovalent salt concentration. The order-disorder transition of representative three-way …