Structure and stability of cytosine deoxyoligonucleotides multiplexes

Abstract

It has very recently been reported that deoxyribonucleic acid oligomers of cytosine with sequences such as d‐T(CN)T aggregate into tetrastranded sructures [J. L. Leroy et al. (1993), Biochemistry, Vol. 32, pp. 6019–6031; K. Gehring et al. (1993), Nature, Vol. 363, pp. 561–565; S. Ahmed (1994), Structural Biology, Vol. 1, pp. 83–88]. Using gel filtration chromatography we have found that the oligomer dC10 aggregates into a mixture of duplex, tetraplex, and octaplex structures. We have also found that at the concentration used for Raman spectroscopy (0.05 M in base residues), these structures remain stable from pH 5 to pH 8 at 5°C. The Raman spectra of these oligomers in a 0.1 M NaCl solution at pH 7 and 5°C show a remarkable resemblance to the Raman spectra of the A‐form double‐helical ribonucleic acid polymer of cytosine taken at pH 5.5 and room temperature [C. H. Chen and G. J. Thomas, Jr. (1977), Biopolymers, Vol. 16, pp. 765–789]. This appears to be the first time that this A‐type furanose ring pucker has been reported in deoxyoligonucleotides in aqueous solution at low salt and pH 5.5–7. The gel filtration chromatography and the uv melting behavior of the annealed dC10 solutions show the presence of an equilibrium mixture of multiplexes with multiple melting transitions. Very slow annealing of dC10 solutions in the pH range 6.5–7.0 also produced a similar equilibrium mixture of multiplexes, but at a much slower rate. Rapidly cooled samples tended to change to the equilibrium mixture over a period of several days. © 1997 John Wiley & Sons, Inc.

Raman, polarized Raman and ultraviolet resonance Raman spectroscopy of nucleic acids and their complexes

“…16,43,50,78,80 An early focus of this body of work was to demonstrate and understand the temperature dependence of nucleic acid Raman spectra (Raman hypochromism), a property which originates from the unstacking and unpairing of the bases as native helical structures are thermally denatured. 4 115,116 Synthetic polynucleotides remain widely used as models for exploring the effects of ions, pH and temperature on nucleic acid conformation. For example, in a recent UVRR study of poly(rI), the conformational effects of metal ion coordination were reported.…”

Ultrafast excited-state dynamics of RNA and DNA C tracts

“…Raman measurements on (dC) 10 were interpreted in terms of a complex equilibrium between duplex, tetraplex, and even octaplex structures [57]. The two-dimensional NMR spectra of Snoussi et al suggest that (rC) 5 adopts multiple intercalation topologies perhaps including an i-motif core terminated by double-stranded hemiprotonated duplexes or unpaired dangling strands [54].…”

Structural Polymorphism of Oligo(dC) with Mixed α,β-Anomeric Backbone

“…At neutral pH self-association of poly(dC) strands persists, even if considerably diminished, as was described for different C-rich sequences (16,18). Rising pH destabilizes CC + base pairs.…”