NMR characterisation of a triple stranded complex formed by homo-purine and homo-pyrimidine DNA strands at 1:1 molar ratio and acidic pH

Abstract

Homo-purine (d-TGAGGAAAGAAGGT) and homopyrimidine (d-CTCCT TI CTTCC) oligomers have been designed such that they are complementary in parallel orientation. When mixed in a 1:1 molar ratio, the system adopts an antiparallel duplex at neutral pH with three mismatched base pairs. On lowering the pH below 5.5, a new complex is formed. The NMR results show the coexistence of a intermolecular pyrimidine.purine:pyrimidine DNA triplex and a single stranded oligopurine at this pH.

Biophysical studies with parallel stranded oligoduplex

“…The probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA, folded and unfolded states (found to be unique for each sequence), that were compatible with CD spectra difference for structural characterization of nucleic acids (Mergny et al, 2005), the alternative conformations that coexist in equilibrium and the range of their fluctuations (Mergny et al, 2005) were described for antiparallel-stranded oligoduplexes. The parallel stranded oligoduplexes were studied before with CD spectroscopy and NMR for structural conformation study (Gundry et al, 2003;Ramsing and Jouim, 1988;Parvathy et al, 2002;Robinson and Wang, 1993;Dolinnya et al, 1997;Aboul-ela et al, 1994;Rippe et al, 1989;Allwi and Santa Licia, 1998;Tchurikov et al, 1989;Bhoumik et al, 1995;Otto et al, 1991;Klysik et al, 1991;Rippe et al, 1992;Williamson, 1994;Wang and Patel, 1994). In this study, the thermal denaturation profiles of parallel stranded oligoduplexes during UV-spectroscopy and fluorescence spectroscopy, for the first time, were shown to follow the similar patterns as were described for antiparallel stranded oligoduplexes.…”

“…These structures of presumptive parallel oligoduplexes were not determined with NMR. NMR data as well as CD data of various parallel oligoduplexes (Gundry et al, 2003;Ramsing and Jouim, 1988;Parvathy et al, 2002;Robinson and Wang, 1993;Dolinnya et al, 1997;Aboul-ela et al, 1994;Rippe et al, 1989;Allwi and Santa Lucia, 1998;Tchurikov et al, 1989;Bhoumik et al, 1995;Otto et al, 1991;Klysik et al, 1991;Rippe et al, 1992;Williamson, 1994;Wang and Patel, 1994). had shown that, despite from the usual Watson-Crick base pairing, these right-handed helical parallel stranded conformation generally included reverse Watson-Crick base pairing, Hoogstein G:C + base pair, Donhue G:C …”

Optimal design of parallel triplex forming oligonucleotides containing Twisted Intercalating Nucleic Acids—TINA

“…TINA has previously been shown not only to stabilize the PT, but also to stabilize the underlying AD ( 1 ). It has been demonstrated that dissociation of PT at acidic pH can occur by (i) dissociation of the triplex strand from the PT complex and thereafter dissociation of the AD at higher temperature, (ii) a simultaneously dissociation of all three strands in the PT and (iii) in rare cases a dissociation of the AD strand of the PT followed by dissociation of the parallel duplex at higher temperature ( 25–30 ). At pH 5.0 we find that TINA modified TFOs can stabilize the whole PT leading to a dissociation T m above the AD T m meaning that the whole PT dissociates simultaneously.…”

Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes

“…The authors explained the similarities as resulting from the coincident helix axes and isostructural nature of the Hoogsteenpaired strands in the two cases, which was later confirmed by crystal structures of two DNA triplexes (39). Whether Watson-Crick or Hoogsteen duplexes are more stable in mixtures of separate strands depends on the sequences and conditions involved (15,18,40). Lavelle and Fresco (18) inferred from optical and thermodynamic studies that the two melting transitions of a d(C + T) 6 *d(AG) 6 12 or r(CU) 12 strands melt with two transitions at low pH.…”