Oligonucleotides duplex formation

In addition to enzymes and other proteins, DNA and RNA have been successfully targeted with DCC systems in several studies. Oligonucleotide duplex formation is a highly efficient means to generate stable complexes even at very low concentration and these complexes can be easily studied by a range of different analytical methods. 

In the thermodynamic study of duplex formation, a variety of complementary pairs of relatively simple, well-defined oligonucleotides are employed, " while the intercalation thermodynamics was examined with more complex or natural DNA duplexes. " Typical intercalating agents examined are acridine orange, acriflabine, actinomycin, daunomycin, ethidium bro-... 

We have investigated the reactions of the COs " radicals with double-stranded DNA by laser flash photolysis techniques [15]. In these time-re-solved experiments, the COs radicals were generated by one-electron oxidation of HCOs by sulfate radical anions, SO4 the latter were derived from the photodissociation of persulfate anions, S20s initiated by 308-nm XeCl excimer laser pulse excitation. In air-equilibrated buffer solution containing the self-complementary oligonucleotide duplex d(AACGCGAATTCGCGTT), 208 , and an excess of HCO3., the decay of the CO3 radical anion absorption band at 600 nm is associated with the concomitant formation of the characteristic narrow absorption band of the G(-H) radicals near 310 nm. 

Forman, J.E., et al. Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays. ACS Symposium Series, 1998, 682, p. 206-228. 

Single-strand oligonucleotides can be dispersed in a two-dimensional matrix of a molecule that resembles the linker unit, in Figs. 6-8 and 6-9, co-mercaptohexanol (MCH). Such a step offers exposed single-strands accessible to duplex formation and other (bio)chemical reactivity. 

---