Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• immobilization of lipo-oligonucleotides carrying a racemic bis(hexadecyloxy)propan-1-yl tag (1a) at the 5’-termini at an artificial lipid bilayer–water phase boundary. These were prepared using the cyanoethyl phosphoramidite 1b. A specific duplex formation with complementary cyanine-5 (Cy5)-labelled DNA strands

• ][22]. This bears the advantage that the target DNA – the presence or absence of which is going to be analysed – should not be labelled separately with a fluorochrome tag such as cyanine-5 (Cy5) or TAMRA, neither by chemical synthesis nor by a polymerase chain reaction (PCR). The chemical formulae (1–3

• + 5 + SG. In a preceeding manuscript we have studied the bilayer incorporation of the lipo-oligonucleotide 4 (5’-d(1a-TAG GTC AAT ACT)-3’) and its successful and specific duplex formation with the cyanine-5-labeled complementary strand 5 (5’-d[(Cy5)-p-AGT ATT GAC CTA]-3’) [19]. As a negative control

Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• tracts by length and composition. This has been demonstrated, for instance, by the inability to distinguish between longer tracts (more than 20–30 base pairs) of homo and alternating distribution of AT base pairs. Our recent studies revealed a novel class of cyanine dyes characterized by bulky

• importance of AT tracts and the selectivity of cyanine dyes. On this basis, we were inspired to prepare the novel binders AP5 with a DBTAA–adenine linker length between AP3 (oligo dT specific) and AP6 (oligo-dT inert) and AP3am, in which pyridinium is exchanged by a permethylated amine, with the aim of