Conformation, dynamics, and structural transitions of the TATA box region of the self-complementary d[C-G)n-T-A-T-A-(C-G)n] duplexes in solution

Abstract

Structural and kinetic features of the TATA box located in the center of the alternating self-complementary d(C-G-C-G-T-A-T-A-C-G-C-G) duplex (TATA 12-mer) and d(C-G-C-G-C-G-T-A-T-A-C-G-C-G-C-G) duplex (TATA 16-mer) have been probed by high-resolution proton and phosphorus NMR spectroscopy in aqueous solution. The imino exchangeable Watson-Crick protons and the nonexchangeable base protons in the TATA box of the TATA 12-mer and TATA 16-mer duplexes have been assigned from intra and inter base pair nuclear Overhauser effect (NOE) measurements. Imino proton line-width and hydrogen exchange saturation recovery measurements demonstrate that the dA X dT base pairs in the TATA box located in the center of the TATA 12-mer and TATA 16-mer duplexes are kinetically more labile than flanking dG X dC base pairs. The proton and phosphorus NMR parameters of the TATA 12-mer monitor a cooperative premelting transition in the TATA box prior to the onset of the melting transition to unstacked strands. Phosphorus NMR studies have been unable to detect any indication of a right-handed B DNA to a left-handed Z DNA transition for the TATA 12-mer duplex in saturated NaCl solution. By contrast, we do detect the onset of the B to Z transition for the TATA 16-mer in saturated NaCl solution. Proton and phosphorus NMR studies demonstrate formation of a loop conformation with chain reversal at the TATA segment for the TATA 12-mer and TATA 16-mer duplexes on lowering the DNA and counterion concentration. The imino protons (10-11 ppm) and phosphorus resonances (3.5-4.0 ppm; 4.5-5.0 ppm) of the loop segment fall in spectral windows well resolved from the corresponding markers in fully paired segments so tha it should be possible to identify loops in longer DNA helixes. The equilibrium between the loop and fully paired duplex conformations of the TATA 12-mer and TATA 16-mer is shifted toward the latter on addition of moderate salt.

Conformation and dynamics of Z-DNA oligomer duplex of d[(CG)3TATA(CG)3] in solution

“…Values of Tms for B-and Z-TATA 16 mer and B-and Z-d(CG)3 are summarized in Table I. The biphasic transitions observed are consistent with the early NMR observation of loop formation in d[CG)2TATA(CG)2] (TATA 12 mer) duplex on decreased oligomer and counterion concentrations (11,19). These results indicate that (i) below the first Tm, Band Z-TATA 16 mer predominantly exist as a duplex; (ii) as the temperature is raised, a transition (the first Tm) from the duplex to a unimolecular hairpin occurs; and (iii) further increase in temperature results in a second transition (the second Tm) from a hairpin to a coiled single strand.…”

“…GHl' in space, consistent with guanine residues in the syn conformation around the (3-glycoside bond, a characteristic of Z-type structures (11). The assigned signals and the chemical shifts are listed in Table II.…”

“…Insertion of dA * dT base pairs into dG * dC stretches in DNA oligomers often prevents the oligomers from exhibiting Z-type structures. For example, the structure and dynamics of a self-complementary d[(CG)3TATA(CG)3] duplex were studied by 'H and 31P NMR to monitor the potential for Z-DNA formation (11). In that study there was, however, no evidence of the B-to-Z transition for the 16 mer, even in saturated NaCl solution, except for a minor peak in the 31P NMR spectrum corresponding to about 11% of the molecules in the Z-form.…”

Structures of mismatched base pairs in DNA and their recognition by the Escherichia coli mismatch repair system.

“…Imino resonances at 10-12 p.p.m. have been observed either for a G*T wobble pair (Patel et al, 1982;Tibanyenda et al, 1984) or for imino protons non-hydrogen bonded in loop structures (Haasnoot et al, 1980(Haasnoot et al, , 1983Patel et al, 1985). To establish the nature of the resonances at high field, we have carried Figure 3a shows the spectrum at this temperature and pre-irradiation for 50 ms at the positions indicated give the difference spectra (Figure 3b and c).…”

Formation of Sequence‐Independent Z‐DNA Induced by a Ruthenium Complex at Low Salt Concentrations

“…42 Since the B–Z transition results from the conformational changes of A and G from anti to syn , AH8–AH1′ and GH8–GH1′ cross‐peaks appear in the NOESY spectra (Figure 4). 43, 44 NOESY experiments without the addition of [Ru(dip) 2 dppz] 2+ were also carried out (Figure S4).…”