Construction and analysis of monomobile DNA junctions

J. H. Chen, M. E A Churchill, T. D. Tullius, N. R. Kallenbach, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

Immobile DNA junctions are complexes of oligomeric DNA strands that interact to yield branched structures in which the branch point cannot migrate. This is achieved by minimizing the sequence symmetry in the flanking arms, so that base pairs lock at the branch site. Here, we report the design, synthesis, and analysis of two semimobile junctions, structures in which a controlled extent of branch point migratory freedom is deliberately introduced. We have constructed two minimally symmetric four-arm semimobile junctions from synthetic deoxy 17-mers. These junctions, termed 'monomobile', contain a single pair of base pairs (A-T or C-G) which can migrate at the site of branching, while the rest of the junction is immobile. We have demonstrated by gel electrophoresis techniques that these junctions form and that they have the predicted 1:1:1:1 stoichiometry. We have compared these junctions with the immobile junction on which they are based, by means of hydroxyl radical protection experiments. From these data, both migratory conformers can be seen to coexist in solution. The semimobile junction with the C-G base pair has the same crossover and stacking pattern observed for the immobile junction, while the junction with the A-T base pair has the opposite pattern. We conclude that crossover and stacking patterns are a direct consequence of the base pairs which flank the junction. In addition, the data indicate that the crossover pattern biases for these junctions are much greater than are the migratory biases.

Original languageEnglish (US)
Pages (from-to)6032-6038
Number of pages7
JournalBiochemistry
Volume27
Issue number16
StatePublished - 1988

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Base Pairing
DNA
Electrophoresis
Stoichiometry
Hydroxyl Radical
Gels
Experiments

ASJC Scopus subject areas

  • Biochemistry

Cite this

Chen, J. H., Churchill, M. E. A., Tullius, T. D., Kallenbach, N. R., & Seeman, N. (1988). Construction and analysis of monomobile DNA junctions. Biochemistry, 27(16), 6032-6038.

Construction and analysis of monomobile DNA junctions. / Chen, J. H.; Churchill, M. E A; Tullius, T. D.; Kallenbach, N. R.; Seeman, Nadrian.

In: Biochemistry, Vol. 27, No. 16, 1988, p. 6032-6038.

Research output: Contribution to journalArticle

Chen, JH, Churchill, MEA, Tullius, TD, Kallenbach, NR & Seeman, N 1988, 'Construction and analysis of monomobile DNA junctions', Biochemistry, vol. 27, no. 16, pp. 6032-6038.
Chen JH, Churchill MEA, Tullius TD, Kallenbach NR, Seeman N. Construction and analysis of monomobile DNA junctions. Biochemistry. 1988;27(16):6032-6038.
Chen, J. H. ; Churchill, M. E A ; Tullius, T. D. ; Kallenbach, N. R. ; Seeman, Nadrian. / Construction and analysis of monomobile DNA junctions. In: Biochemistry. 1988 ; Vol. 27, No. 16. pp. 6032-6038.
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