8 research outputs found
Construction and Assembly of Chimeric DNA: Oligonucleotide Hybrid Molecules Composed of Parallel or Antiparallel Duplexes and Tetrameric iâMotifs
Chimeric
DNA containing parallel (ps) and antiparallel
(aps) duplex
elements as well as poly-dC tracts were designed and synthesized.
Oligonucleotide duplexes with ps chain orientation containing reverse
WatsonâCrick dA-dT base pairs and short dÂ(C)<sub>2</sub> tails
are stabilized under slightly acidic conditions by hemiprotonated
dCH<sup>+</sup>-dC base pairs (âclampâ effect). Corresponding
molecules with aps orientation containing WatsonâCrick dA-dT
base pairs do not show this phenomenon. Chimeric DNA with ps duplex
elements and long dÂ(C)<sub>5</sub> tails at one or at both ends assemble
to tetrameric i-motif structures. Molecules with two terminal dÂ(C)<sub>5</sub> tails form multimeric assemblies which have the potential
to form nanoscopic scaffolds. A preorganization of the ps duplex chains
stabilizes the i-motif assemblies up to almost neutral conditions
as evidenced by thermal melting and gel electrophoresis. Although,
ps DNA is generally less stable than aps DNA, the aps duplexes contribute
less to the stability of the i-motif than ps DNA