Conformational analysis of the dinucleotides 5′‐methylphospho‐N⁶‐dimethyladenylyl‐uridine (mpm⁶₂A‐U) and 5′methylphospho‐uridylyl‐N⁶‐dimethyladenosine (mpU‐m⁶₂A) and of the trinucleotide U‐m⁶₂A‐U

Abstract

NMR and CD studies were carried out on the dinucleotides 5'-methylphospho-N 6-dimethyladenylyl-uridine (mpmf-U) and 5'-methylphospho-uridylyl-N6-dimethyladenosine (mpU-mZ A) and on the trinucleotide U-mzA-U.A detailed comparison is given of the conformational features of mpmfA-U and mpU-m$A with the corresponding 5'-nonphosphorylated dinucleotides mqA-U and U-mqA, respectively. The behaviour of the trinucleotide U-mzA-U is compared with the properties of the constituent dinucleotides U-mqA and mpmq A-U.Chemical-shift and CD data were used to determine the amount of stacking interactions. For each compound NMR spectra were recorded at two or three sample concentrations in order to separate intermolecular and intramolecular base-base interactions. The coupling constants of the ribose ring are interpreted in terms of the N/S equilibrium, and population distributions along the backbone angles fl, y and E are presented.The combined data indicate a strong similarity between mpmqA-U and m$A-U both in degree and in mode of stacking. In contrast, the existence of different types of stacking interactions in mpU-m$A and U-mzA is suggested in order to explain the NMR and CD data. It is concluded that dinucleoside bisphosphates serve better as a model for the behaviour of trinucleotides than dinucleoside monophosphates.The trinucleotide U-mqA-U adopts a regular single-stranded stacked RNA structure with preference for N-type ribose and y+ and p' backbone torsion angles. The difference in behaviour between the U-mfA-part of U-mfA-U and the dimer U-mzA is seen as a typical example of conformational transmission.The biological activity of polynucleotides is determined mainly by the three-dimensional structure of these polymers. It is well known that the vertical base-base stacking constitutes a dominant driving force in the formation of stable RNA and DNA structures. For example, in the case of the codonanticodon interaction, the stacking energies of the participant bases are crucial for the conformation of the anticodon loop and the codon-anticodon complex [l, 21. This might be an important feature for the translation activity.Seen in this light, studies of the conformational behaviour of single-stranded oligonucleotides pursued in this laboratory and elsewhere are quite useful because these yield valuable information about stacking properties. Of special interest are differences in behaviour between dinucleoside monophosphates, trinucleotides, tetranucleotides and longer oligomers.Correspondence to C. Altona, Gorlaeus Laboratories, P.O. Box 9502, NL-2300 RA Leiden, The Netherlands Note. This is part 54 of the series Nucleic Acid Constituents from this laboratory, part 53 will appear later [Orbons, L. P. M., van Such studies may provide insight into the factors important for base-base stacking, like base sequence, electrostatic repulsion between the phosphate groups, conformational preferences of the sugar ring and backbone chain, and conformational transmission effects.For example, 'H-NMR [3 -51 and CD [6] investigations c...

Protein resonance assignment by BSH‐CP‐based 3D solid‐state NMR experiments: A practical guide

“…The following equation for temperature calibration (Equation ) also takes the effect of pH and salt concentration (c salt , in mM) into account and is valid in the range 0–80°C, from pH units 2 to 7, and for salt concentrations from 0.0 to 1.0 M. …”