Nearest‐neighbor and next‐nearest‐neighbor effects in the proton NMR spectra of the oligoribonucleotides ApXpG, CpXpG, CpApXpUpG, ApGpXpC, and ApGpXpCpU

Abstract

The proton nmr spectra of the oligoribonucleotides in the series CpXpG, ApXpG, CpApXpUpG, and ApGpXpC (X = A, G, C, and U), together with the reference compounds CpG, ApG, CpApUpG, and ApGpC, have been measured. A complete analysis of all the nonexchangeable base protons and the ribose H‐1′ protons was made. The insertion of a nucleotide X into a oligoribonucleotide led to shift changes at both nearest‐neighbor and next‐nearest‐neighbor positions, which were rationalized in terms of the shielding abilities of the various bases. The derived shielding trends in the ApGpXpC series of compounds were successfully used to predict the chemical shifts of resonances in the related ApGpXpCpU series.

The application of double-quantum and spin echo nuclear magnetic resonance spectroscopy to the assignment of 1H chemical shifts of RNA oligomers

“…In the first experiment the highest field pair of H-6 (7.680 ppm) and H-5 (5.799 ppm) doublets were assumed to arise from U(1) since this assignment agreed with the previous results for 5' terminal pyrimidines ( Table 1). The U(l) protons should also experience the ring current shielding effect of the 3' adenosine (22,23). The double-quantum spectrum verified the above assumption; however, no other transitions were observed.…”

“…Removal of the U and C(2)H-5 resonances revealed H-1' doublets at 5.882 and 5.863 ppm (U and GH-1', respectively). The H-1' chemical shifts in Table 2 trends (22,23).…”

“…In the region containing the anorneric proton signals of UpUpU only one H-1' doublet at 5.868 ppm could be identi- Assignment of the base chemical shifts to specific uridine residues (Table 1) shielding effect on neighbouring bases in a weakly stacked UpUpPy (Py = pyrimidine) sequence at high temperatures (22,23). The H-1' resonances were only tentatively assigned by comparison with data from UpUpC and UpU.…”

“…The doublets at 7.77 ppm result from the overlap of the UH-6 and C(2)H-6 resonances. Differentiation of the two cytidine H-6 doublets was based on the shielding effect of the neighbouring guanosine on the C(2) base protons (22,23). The doublet at 6.024 ppm was assigned to C(4)H-5, while the C(2)H-5 signal was overlapped with H-1' resonances between 5.87 and 5.94 ppm.…”

“…Assignment of the U(5) and U(6) base protons (Table 2) relied on the next-nearest-neighbour shielding effect of G(3) (22,23) on the chemical shifts of the U(5)H-6 and H-5 protons. These assignments also follow from comparison with data on ApGpCpU (25).…”