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Chapter 5 : Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies)

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Abstract:

The location and identity of a large number of the modified nucleosides found in tRNA are highly conserved across diverse species and between tRNA isoacceptors. Conserved modification patterns in rRNAs and small nuclear RNAs also suggest that particular modified nucleosides have critical roles, although these functions are not well described compared to modifications found in tRNA. The nuclear magnetic resonance (NMR) determined biophysical properties have also provided an explanation for changes in important functions of tRNA during protein synthesis such as codon-anticodon recognition. This chapter talks about NMR determination of nucleoside conformation. The use of the percentage of 3'-endo sugar conformation as a measure of base stacking originated from NMR investigations on ribonucleotide dimers and trimers. Nucleoside modification in either the base or sugar can have significant effects on the sugar conformation, the glycosyl conformation, and base stacking. The 3'-gauche effect is mechanistically related to the anomeric effect in that it arises due to a geometrically dependent overlap between σ* and n lone pair molecular orbitals. Nucleoside bases that are in a stacked geometry generally have aromatic NMR proton shifts that are upfield of the positions seen in the absence of significant stacking. The chapter also focuses on conformational and thermodynamic effects of specific nucleoside modifications. Our knowledge of the fundamental biophysical properties of modified nucleosides will be critical to understanding how modification has been used throughout biology to optimize the function of biochemically critical processes involving RNA.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5

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Figures

Image of Figure 1
Figure 1

The two limiting conformations for ribonucleosides. (A) 2′-endo sugar with the base in the pseudoequatorial conformation; (B) 3′-endo sugar with the base pseudoaxial.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
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Image of Figure 2
Figure 2

NMR NOE experiments are used to define the glycosyl conformation for nucleosides. The interproton distances between the base H6 (pyrimidines) or H8 (purines) and the sugar protons change as a function of glycosyl angle. The figure shows the key distances involving Η1′, H2′, and H3′ protons for adenosine and how they differ for either the or conformations.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
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Image of Figure 3
Figure 3

Molecular orbital interactions in pyrimidines that affect the thermodynamically preferred glycosyl conformation and change upon modification. Both the anomeric interaction and an interaction involving the H5-H6 bond are affected by modification. For the anomeric effect, the lone pair electrons at O4′ are in an np orbital which overlaps with the * orbital at C1′. In the 3′-endo conformation (shown) the C1′-N bond is axial and the * orbital oriented along the glycosyl bond can bond in a -like fashion with the np orbital. The same O4′ lone pair orbitals can interact with * antibonding orbitals from the pyrimidine H5-H6 double bond. An electron withdrawing group (EWG) at the 5 position increases the size of the * orbital on H6 as shown which would increase the intetaction and favor a 3′-endo conformation with a low angle.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
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Image of Figure 4
Figure 4

Watson-Crick sU-A base pair and reversed Hoogsteen sU-A base pair. The s modification in a non-hydrogen bonding position has a direct effect on base stacking and strongly promotes the 3′-endo sugar conformation.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
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Image of Figure 5
Figure 5

Three-dimensional structure of the ρΑρ dinucleotide step in a standard Α-form geometry. The coordinated water molecule stabilizes the N1-H imino proton against facile exchange with bulk solvent and coordination to the phosphate backbone restricts the base conformation and the backbone 5′ to the modification site.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
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Image of Figure 6
Figure 6

The anticodon domains of tRNA and tRNA shown in panel A have pseudouridines at positions 39 and 35, respectively. As a model system for the codon-anticodon interaction where would either be remote from the anticodon triplet as in tRNA or within the anticodon triplet as in tRNA, the two RNA hairpins in panel were used to demonstrate stabilization for modification adjacent or within the double-stranded region. Pseudouridine results in an increase in the of 2.6 and 5.5°C for the tRNA and tRNA tetraloop hairpins, respectively.

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5
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Tables

Generic image for table
Table 1

Modification effects on the 2′-endo/3′-endo sugar conformational equilibrium thermodynamics

Citation: Davis D. 1998. Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies), p 85-102. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch5

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