RNA Riboswitch containing unnatural nucleobase pair
Sarabjeet Seehra '16
A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair; Hernandez, A. R.; Shao, Y.; Hoshika, S.; Yang, Z.; Shelke, S. A.; Herrou, J.; Kim, H. J.; Kim, M. J.; Piccirilli, J. A.; Benner, S. A.. Angew. Chemie - Int. Ed. 2015,
54 (34), 9853â9856
Contents:
I. Introduction
The idea of increasing the number of replicable nucleotides in DNA and RNA has been a topic of interest in synthetic biological/chemical research for over two decades. In particular, modification of nucleotide base pairs on RNA are structurally more
important due to the increase in conformational freedom as a result of the 2'-hydroxyl group. One strategy used to increase the nucleobase library, called "artificially expanded genetic information system (AEGIS)"involves designing nucleotide base pairs with
specific size, geometry and hydrogen bond specifications that resemble Watson-Crick base pairing geometry.
An unnatural base pair between 6- amino-5-nitro-3-(1'-b-d-ribo-furanosyl)-2(1H)-pyridone and 2-amino-8-(1'-b-d-ribo-furanosyl)-imidazo-[1,2-a]-1,3,5-tria-zin-4-(8H)-one (called a Z and P base pair)is being shown
in a spacefill model of with the atoms colored according to cpk convention with the hydrogens omitted. The carbons are grey, the nitrogens blue, oxygen red, phosphorus yellow.The unnatural base pairs are displayed in purple.In this tutorial, the effect of
replacing a C:G base pair with a Z and P base pairing interaction to the function of a 67 nucleotide xpt-pbuX riboswitch aptamer domain in binding a hypoxanthine ligand.
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Z:P unnatural base pairing and base stacking interactions
As further clarification, AEGIS involves attempting to fit a base pair to Watson-Crick base pair geometry, as well as incorporate a other pairing specifications. First, you have size complementarity, in which a large purine interacts with a
small pyrimidine. Below are some examples of artificial base pairs created using the AEGIS method (denoted in purple), compared to the standard Watson Crick Base Pairs (in green).![]()
Depiction of the Z and P base pairing interaction in riboswitch aptamer. Notice that both the Z and P unnatural bases adopts a c3'-endo conformation, which conforms to characteristics of A-DNA. Also notice that the G:C hydrogen bonding interactions
is retained in the Z:P interactions, rather than pairing via hydrophobic interactions.
Base stacking interaction between Z and adjacent A base. Notice that the nitro group (labeled in yellow) of the Z base lies in the plane of the adenine base, suggesting it might play a role in base stacking interactions.
Electron Density Map of Z:P base pair. The 2mFo-DFc maps, are contoured at an isovalue of 1.0 and shown in purple. Notice that there is electron density at the C5 position (at the nitro group) in the Z base that was not present in the prior C:G base
pair. This supports the nitro group is involved in base-stacking interactions.
Locations of bound water molecules in pink.
Locations of bound water molecules on solvent accessible surface in pink.
Location of phosphate oxygens shown in red, phosphorus in yellow.
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Ligand binding interaction with riboswitch and structural
DNA adopts the c2'-endo conformation that results in the longest possible phosphate phosphate distance so that the phosphates point out and can be well hydrated.
Base pair in DNA showing 2'-endo sugar conformation on G, but C1'-exo conformation on the C
Base pair stacking at Purine Pyrimidine step showing intrastrand base stacking showing propellar twist and major groove purine purine clash.
Base pair stacking at Pyrimidine Purine step showing interstrand base stacking and minor groove purine purine clash.
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IV. Conformational analysis of backbone
The major conformations of the DNA phosphodiester backbone are generally typified by low energy anti butane conformations except for the O5'-C5'-C4'-C3' conformation which is gauche+ and the phosphodiester bonds which are governed by the anomeric
effect and are gauche-
This is the alpha torsion bond which you can see is gauche- because of the anomeric effect
This is the beta torsion bond which you can see is anti which minimizes the energy based on sterics
etc etc etc.
This is the gamma torsion bond which you can see is gauche+ so as to allow DNA double helix to form
This is the delta torsion bond which you can see is trying to be anti and is governed by the 5-membered ring
This is the epsilon torsion bond which you can see is anti to minimize steric effects
This is the zeta torsion bond which you can see is gauche- because of the anomeric effect
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V. TOPIC 5
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VI. References
PDB Reference
PubMed Ref
Reference 3
Reference 4
Reference 5
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