803724-03-0Relevant articles and documents
Cooperative melting in caged dimers with only two DNA duplexes
Eryazici, Ibrahim,Prytkova, Tatiana R.,Schatz, George C.,Nguyen, Sonbinh T.
, p. 17068 - 17070 (2010)
Small molecule-DNA hybrids with only two parallel DNA duplexes (rSMDH 2) displayed sharper melting profiles compared to unmodified DNA duplexes, consistent with predictions from neighboring-duplex theory. Using adjusted thermodynamic parameters obtained from a coarse-grain dynamic simulation, the experimental data fit well to an analytical model.
Design of an intercalating linker leading to the first efficiently 5′,5′-linked alternate-strand Hoogsteen triplex with high stability and specificity
Jessen, Carsten H.,Pedersen, Erik B.
, p. 2465 - 2471 (2004)
This is the first report describing the design, synthesis, and incorporation of an intercalating linker leading to an efficiently 5′,5′-linked alternate strand Hoogsteen triplex. Using molecular modeling, the 5′.5′ problem was solved in a rather simple way. The two relatively distant 5′-ends have been connected with a molecule that provides rigidity to the structure, while being flexible enough to allow stacking upon all four strands. The synthesis of the core of the designed molecule was conducted by Sonogashira coupling of an appropriately substituted iodobenzene with 1,3-diethynylbenzene to give a conjugated system with three benzene rings interconnected with triple bonds. For the alternate-strand triplex obtained with the intercalating linker, the stability obtained is higher than that of the corresponding homotriplex of equivalent total length and with the same nucleotides. This is deduced from a 5° higher melting temperature of the alternating triplex. The sensitivity towards mismatches in the alternate-strand triplex is in the same range (ΔTm = -13° to -19°) as those observed for homotriplexes.
