scholarly journals Classification of RNA backbone conformation into rotamers using 13C′ chemical shifts: How far we can go?

2019 ◽  
Author(s):  
A. A. Icazatti ◽  
J.M. Loyola ◽  
I. Szleifer ◽  
J.A. Vila ◽  
O. A. Martin
Keyword(s):  
Chemical Shifts ◽  
Conformational Space ◽  
Phosphate Backbone ◽  
Ribose Phosphate ◽  
Conformational Preferences ◽  
Backbone Conformation ◽  
Rna Backbone ◽  
Rna Backbone Conformation ◽  
Torsional Angles

ABSTRACTThe conformational space of the ribose–phosphate backbone is very complex as is defined in terms of six torsional angles. To help delimit the RNA backbone conformational preferences 46 rotamers have been defined in terms of the these torsional angles. In the present work, we use the ribose experimental and theoretical 13C′ chemical shifts data and machine learning methods to classify RNA backbone conformations into rotamers and families of rotamers. We show to what extent the use of experimental 13C′ chemical shifts can be used to identify rotamers and discuss some problem with the theoretical computations of 13C′ chemical shifts.

scholarly journals Classification of RNA backbone conformations into rotamers using 13C′ chemical shifts: exploring how far we can go

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7904 ◽  
Author(s):  
Alejandro A. Icazatti ◽  
Juan M. Loyola ◽  
Igal Szleifer ◽  
Jorge A. Vila ◽  
Osvaldo A. Martin
Keyword(s):  
Machine Learning ◽  
Chemical Shifts ◽  
Conformational Space ◽  
Machine Learning Methods ◽  
Phosphate Backbone ◽  
Ribose Phosphate ◽  
Conformational Preferences ◽  
Rna Backbone ◽  
Torsional Angles

The conformational space of the ribose-phosphate backbone is very complex as it is defined in terms of six torsional angles. To help delimit the RNA backbone conformational preferences, 46 rotamers have been defined in terms of these torsional angles. In the present work, we use the ribose experimental and theoretical 13C′ chemical shifts data and machine learning methods to classify RNA backbone conformations into rotamers and families of rotamers. We show to what extent the experimental 13C′ chemical shifts can be used to identify rotamers and discuss some problem with the theoretical computations of 13C′ chemical shifts.

scholarly journals Convertible and Constrained Nucleotides: The 2’-Deoxyribose 5’-C-Functionalization Approach, a French Touch

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 5925
Author(s):  
Crystalle Chardet ◽  
Corinne Payrastre ◽  
Béatrice Gerland ◽  
Jean-Marc Escudier
Keyword(s):  
Nucleic Acid ◽  
Conformational Space ◽  
Biological Applications ◽  
Sugar Phosphate ◽  
Conformationally Constrained ◽  
Precise Control ◽  
Phosphate Backbone ◽  
Nucleophilic Displacement ◽  
Torsional Angles ◽  
Biotechnical Properties

Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson–Crick base-pairing. We show that 5’-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5’-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.

RNA backbone rotamers – finding your way in seven dimensions

2005 ◽  
Vol 33 (3) ◽  
pp. 485-487 ◽  
Author(s):  
L.J.W. Murray ◽  
J.S. Richardson ◽  
W.B. Arendall ◽  
D.C. Richardson
Keyword(s):  
Rna Catalysis ◽  
Noise Levels ◽  
Base Interaction ◽  
Empirical Distributions ◽  
Chemical Residues ◽  
Backbone Conformation ◽  
Backbone Dihedral Angle ◽  
Rna Backbone ◽  
Rna Backbone Conformation ◽  
Quality Filtering

Despite the importance of local structural detail for a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been recalcitrant to analysis. There are too many variable dihedral angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor and all-atom-steric clashes) to the backbone dihedral angle distributions from a selected 8636 residue RNA database. With noise levels significantly decreased, clear signal appears for the underlying angle preferences. We analyse the multidimensional backbone dihedral distributions within sugar-to-sugar ‘suites’ rather than chemical residues due to the greater base interaction and steric interdependence within the suite. The final result is a small library of RNA backbone rotamers, each represented by a data cluster in seven-dimensional dihedral space, which should provide valid conformations for nearly all RNA backbones encountered in experimental structures. We are in the process of improving that library, and developing tools and applications for it in structure determination and analysis.

Molecular contacts of ribose-phosphate backbone of mRNA with human ribosome

2015 ◽  
Vol 1849 (8) ◽  
pp. 930-939 ◽  
Author(s):  
Dmitri E. Sharifulin ◽  
Anastasia S. Grosheva ◽  
Yulia S. Bartuli ◽  
Alexey A. Malygin ◽  
Maria I. Meschaninova ◽  
...  
Keyword(s):  
Phosphate Backbone ◽  
Ribose Phosphate

Proximity effects in 29Si, 13C, and 1H NMR spectra of ortho substituted phenoxytrimethylsilanes

1990 ◽  
Vol 55 (8) ◽  
pp. 2019-2026 ◽  
Author(s):  
Jan Schraml ◽  
Václav Chvalovský ◽  
Harald Jancke ◽  
Peter Koehler ◽  
Mikhail F. Larin ◽  
...  
Keyword(s):  
Oxygen Atom ◽  
1H Nmr ◽  
Proximity Effect ◽  
Nmr Spectra ◽  
Chemical Shifts ◽  
Proximity Effects ◽  
1H Nmr Spectra ◽  
Methyl Groups ◽  
Conformational Preferences

NMR Spectra of eight ortho substituted phenoxytrimethylsilanes, 2-X-C6H4-OSi(CH3)3 (X = Cl, Br, OCH3, NH2, NO2, OSi(CH3)3, CH3, and H), are reported. In contrast to analogous ortho substituted methoxybenzenes the 13C chemical shifts of C-2 and C-6 aromatic carbons do not exhibit consistent trends indicating different conformational preferences in the trimethylsiloxybenzenes. Under the influence of the ortho substituents the nuclei of OSi(CH3)3 group (29Si, 13C, and 1H) are deshielded; compounds with X = CH3 (and H) appear anomalous in this respect. It is argued that this proximity effect is not due to an interaction involving terminal methyl groups but involves the oxygen atom of the OSi(CH3)3 group; it is most likely due to an interaction with unshared electrons of the ortho substituent.

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