"Alternating B-DNA" conformation for the oligo(dG-dC) duplex in high-salt solution.

Abstract

The high resolution IH and 31P NMR spectra of the (dG-dC)8 duplex have been recorded in low-and high-salt solutions in order to evaluate the structural aspects of the saltinduced transition of oligo (dG-dC) (2) demonstrated that the circular dichroism of oligo(dG-dC) and poly(dG-dC) inverts in the presence of a high salt concentration. This reversible transition exhibits an activation energy of 22 kcals in both directions (2). The conformational transition was also observed when 60% (final concentration) ethanol (3) or the antibiotic mitomycin was added to poly(dG-dC) in aqueous solution (4). The trypanocidal agent ethidium bromide binds to the low-salt form of poly(dG-dC) more strongly than to the high-salt form (5). The salt-induced transition was not observed for the synthetic RNA poly(G-C) or the synthetic DNAs poly(dA-dT) and poly(dG)-poly(dC) (2). These results suggest that conformational features related to helical type, base composition, and base sequence play a crucial role in governing the presence or absence of the structural transition.Drew et al. (6) have observed that crystals of dC-dG-dC-dG grown in low-and high-salt solutions exhibit different space groups, and they demonstrated a reversible transition between the two crystalline states.We have monitored the 'H and 31p NMR parameters for (dG-dC)n as a function of salt concentration in an attempt to elucidate the structural aspects of the salt-induced conformational transition. Because the NMR line widths are narrower at the oligomer level, this paper discusses the NMR chemical shifts for oligo(dG-dC) of chain lengths 16 and 20-30. EXPERIMENTALThe isolation and characterization of (dG-dC)n oligomers of chain lengths 16 (n = 8) and 20-30 (n = 10-15) have been reported (7). They were passed through Sephadex GlO columns prior to the recording of NMR spectra.High-resolution 360-MHz proton NMR spectra were recorded in the continuous wave (CW) mode for the exchange- (Fig. 1). The base protons can be readily assigned, whereas it is not yet possible to definitively differentiate among protons on the sugar ring linked to the guanosine and cytidine residues. The cytidine H-5 and H-6 protons, which shift upfield on duplex formation, are sensitive indicators of base pair overlap geometries in the duplex state. By contrast, the sugar H-i' chemical shifts predominantly monitor changes in the glycosidic torsion angles associated with the duplex-tostrand transition.The magnitude and direction of the chemical shift changes associated with the duplex-to-strand transition of (dG-dC)8 (Fig. 1) and poly(dG-dC) are similar to values reported for the melting transition of poly(dA-dU) (8), poly(dA-dT) (8), and poly(dI-dC) (9). These alternating purine-pyrimidine polynucleotide duplexes adopt B-DNA type overlap geometries in solutions (8, 10).Salt-Induced (dG-dC)8 Transition. Circular dichroism spectra have been recorded for oligo(dG-dC) duplexes as a function of salt concentration. The extent'of the structural transition for (dG-dC)8 as a function of NaCl is...

Lack of Z-DNA conformation in mitomycin-modified polynucleotides having inverted circular dichroism.

“…[Recently a similar inhibition of the B-UZ transition was observed in aflatoxin B1-poly(dG-dC).poly(dG-dC) complexes (22 (5,15,16). Only one peak is evident, however, at the position of that of the control (4.30 ppm).…”

Conformational transitions of poly(dA-dC).poly(dG-dT) induced by high salt or in ethanolic solution

“…If a. transition from the right-handed B helix to the left-handed Z-type form is present as it was found in fibres (8) and for poly(dG-dC).poly(dG-dC) in solution (7,(9)(10)(11)(12), the purine-pyrimidine dinucleotide may have a 2'-endo pucker at the pyrimidine and a 3'-endo or 1'-exo pucker at the purine site. Insertion of A-T pairs between C-G pairs introduces alterations in the duplex geometry compared with poly(dG-dC).poly(dG-dC) which can explain deviations in the inverted CD spectra of the two duplex polymers ( fig.…”

31P-NMR analysis of the B to Z transition in double-stranded (dC-dG)3, and (dC-dG)4in high salt solution

“…Also, 31P NMR spectra of the left handed Z DNA of polynucleotides show two characteristic signals with separation or ca. 0.5-1.5 ppm, which can be used to detect the presence of Z DNA in solution (3,6,8,9,(15)(16)(17)(18)(19)(20)(21)(22)(23). It is usual to assume that the downfield and upfield components correspond to predominantly gt and gg conformations, respectively, of the i and a torsion angles (24) in the 03'-P-05' linkages (6,(15)(16)(17)(18)(19)(20)(21)(22)(23) …”