¹³C-NMR of Ribosyl ApApA, ApApG and ApUpG

Abstract

The chemical shifts as well as the 13C-31P coupling constants of the carbon-13 nuclei in single-stranded ApApA, ApApG, and ApUpG are sensitive to sequence and temperature. ApApA and ApApG have similar properties with large shielding (up to 1.7 ppm) of many of the base carbons upon decreasing the temperature from 70 degrees C to 11 degrees C; the base carbons have smaller shielding changes in ApUpG. Large shielding and deshielding effects are observed for the 1', 3', 4' and 5'-carbons over this temperature range. Analysis of the 13C-31P couplings measured at the 4' ribose carbons show that the population of the anti rotamer about O5'-C5' varies from 98 to 75%, and is higher in ApApA and ApApG than in ApUpG. The CCOP coupling data at 2' and 4' is consistent with a blend of the -antiperiplanar/-synclinal nonclassical rotamers about the C3'-O3' bond, varying from 89/11% in ApApG to 55/45% in ApUpG. The coupling and chemical shift data support the thesis that ApUpG is stacked much less than the other two molecules. The stacked forms of all three trinucleotides is most easily interpreted by a standard A-RNA model. It is not necessary to invoke the "bulged base" hypothesis [Lee, C.-H. and Tinoco, Jr., I. (1981) Biophysical Chemistry 1, 283-294; Lankhorst, P.P., Wille, G., van Boom., J.H., Altona, C., and Haasnoot, C.A.G. (1983) Nucleic Acids Research 11, 2839-2856] to explain the contrast in 13C spectroscopic properties of ApUpG in comparison to ApApG and ApApA.

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,1H-NMR Spectroscopy and Monte Carlo Simulations

“…An experimental estimate of -rc in the case of slow internal motion can be extracted from the plot of the ratio of selective (s) and non-selective (ns) spectral densities (38): [14] which can also be expressed as a function of overall tumbling using equation [12] :…”

“…For the slow internal motion model and isotropic tumbling the spectral densities were : (12] In the case of the fast internal motion model, the expression for the spectral densities (37) was:…”

“…In contrast, only the classical A-RNA helix conformation was described in an NMR study of the tetramer r(AACC) (II). Moreover, the existence of bulged structures has been questioned in a report (12) on the heteronuclear NMR data of RNA trimers and no evidence for bulged uridyl residues was found for the r(CAUG) tetramer (13). Although a considerable amount of experimental NMR data for short oligonucleotides has been given in all these studies, either the corresponding conformational analyses have relied on only a few NMR parameters (principally, 3 Jl'2' and 3 lu values and trimerization shifts) or the local conformation about each of the torsion angles has been considered separately.…”

High‐Resolution Studies of Uniformly 13C,15N‐Labeled RNA by Solid‐State NMR Spectroscopy

“…Binding of Na + ions caused by charge aggregation and formation of Bjerrum ion pairs could shift the signals of the sugar backbone downfield, similar to the case of single nucleotides. [28] Stacking in nucleic acids is known to shift the 13 C resonances of the nucleobases upfield, [29] while hydrogen bonding of the adjacent heteroatoms causes the opposite, downfield shifts. [30,31] In the 14-mer RNA, the C2, C4, C5, and C8 resonances of A4 are shifted upfield relative to free ATP, while the C6 resonance is shifted downfield (see Table S2 in the Supporting Information).…”

Hochauflösende Festkörper‐NMR‐Spektroskopie an vollständig 13C,15N‐markierter RNA

“…Es ist bekannt, dass Stapeleffekte in Nukleinsäuren die Resonanzen der Kohlenstoffatome in der Nukleobase hochfeldverschieben, [29] während Wasserstoffbrücken der benachbarten Heteroatome umgekehrt eine Tieffeldverschiebung bewirken. [30,31] In der 14-meren RNA sind die C2-, C4-, C5-und C8-Resonanzen des Nukleotids A4 gegenüber freiem ATP hochfeldverschoben, während die C6-Resonanz tieffeldverschoben ist (Tabelle S2).…”