Rafael B.

Navarro, 2007-08 18 1, MS Biochemistry CHEM 266: Chemistry of Nucleic Acids; Report; 15 January 2013

Journal Article: Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone (Sheng, Jia et al. Nucleic Acids Research, 2012, Vol. 40, No. 16 pp. 8 1 1 1–81 18)

Introduction
Ribonucleic acid or RNA plays important roles in various biological activities. Primarily, these nucleic acids are the key components in protein translation; moreover, they could also perform catalysis just like protein enzymes and could regulate gene expression in cells. These molecules were also hypothesized to be the precursors of life on Earth since they can perform autocatalysis, self-replication, and autopoiesis in prebiotic Earth conditions. They are copolymers of ribonucleotides that are composed of three components: nitrogenous bases, a ribose sugar, and phosphate. The composition, sequence, and interaction between functional groups are keys to the folding of the macromolecule which is critical to its biological activity. RNA has different forms and focusing only in protein expression in cells, a type of RNA, the messenger RNA (mRNA) carries the code for the sequence of the protein while transfer RNA reads the code in the

With these technologies. A-U. which are created after posttranscriptional modification of RNA especially tRNAs. 2012). Wobble base pairing differs from Watson-Crick base pairing where the former involves diverse combinations of bases whereas the latter is only limited to A-T. Using the data from the crystallographic . different secondary structures of ribonucleic acids plus the posttranscriptional modifications of these molecules can now be easily discovered. and base pairing with modified nucleotides like 5-methoxy-uridine. Nucleotides with covalent alterations are also essential to tRNA folding and their capacity to perform codon reading using wobble base pairing (Takai and Y okoyama. The structure of ribonucleic acids can now be easily determined with some physical methods such as x-ray crystallography. 2006). The diverse combinations in wobble base pairing is important because there are sixty-one codons that correspond to an amino acid yet there are only forty-five or less number of anticodons carried by amino acyl tRNAs in each organisms. and G-C. The RNA folding pattern and codon reading depends on the hydrogen-bonding interactions between nucleobases in the nucleic acid and these interactions are called wobble base pairing.mRNA and carries the amino acid that is used for the synthesis of proteins (Blackburn et al. Novoa et al. 2003. Wobble base pairing also involves pseudouracil. dihydroxyuridine.

the tRNAs in prokaryotes and in eukaryotes were found to be the most modified nucleic acid. current technologies such as automated oligonucleotide synthesizers help researchers to study specific nucleotide sequences and those with intentionally altered functional groups to discover novel intramolecular interactions at the atomic level (Sheng et al. Furthermore. and proline. 2007). In addition. 2010). 5-methoxyuridine. there are about 109 natural RNA modifications registered in the database and most of these are alterations found in nucleobases. in prokaryotes including Gram-positive bacteria and Gram-negative bacteria. 201 1). Reports also show that tRNAs with 5-methoxyuridine as part of their anticodon can carry different amino acids such as alanine. threonine. serine. In addition. Many researches have talked about the discovery of the modified nucleoside. So far. one can also calculate and visualize the electronic structures and interactions among atoms in the molecule using softwares that incorporate algorithms involving quantum mechanical theory (Sheng and Huang. uracil is the most modified nucleobase among others according to the database (Cantara et al. the discovered natural RNA modifications are currently organized and readily accessible in the RNA Modification Database (RNAMDB). This modified nucleobase was also found to have greater wobble base . valine.techniques. Additionally. Summary of the Research Background.

As a result. The purified oligonucleotides were crystallized and subjected to anomalous scattering method of x-ray crystallography and the three-dimensional structures were determined using software with algorithm that involves density functional theory. 2' -SeMe to maintain the A-form plus 5-methoxyuridine (others have replacement of O atom with S and Se) using phosphoamidite method in an automated synthesizer. 1999). This study aimed to determine the three-dimensional structure of an oligonucleotide with the modification using x-ray crystallographic technique and molecular modeling to understand the role of the functional group modification in base pairing at the atomic level. They were also able to synthesize oligonucleotides with Omethyl as well as S-methyl and Se-methyl to understand the role of oxygen in stabilizing the structure of the oligonucleotide and its role in base pairing. the authors of this study previously found that there were no threedimensional structure of oligonucleotides containing 5-methoxyuridine determined yet so the role of the 5-methoxy functional group in wobble base pairing had not yet been elucidated. Despite the fact that 5-methoxy modification has been studied. Methodology. The oligonucleotides were also subjected to UV .pairing efficiency than uracil (Takai et al. then purified in HPLC. scientists hypothesized that the 5-methoxy functional group has great effect on the wobble base pairing ability of the tRNA especially during protein translation. The researchers were able to synthesize an RNA-like duplex A-DNA with deoxyuracil modified with.

In contrast. this interaction was not observed in oligonucleotides with 5-methylsulfur and 5-methylselenium groupcontaining modified uridine. . may facilitate base recognition between the anticodon of tRNA and codon of mRNA through efficient wobble base pairing. This hydrogen bonding was not found however in the oligonucleotides with the sulfur and selenium replacements. the three-dimensional structures of oligonucleotides were compared with each other. the hydrogen-bond also make the 5-methoxy group and the uracil base assume a coplanar conformation relative to each other thus making the base stacking of the whole oligonucleotide very rigid as evidenced by both crystallography and molecular modeling results. As a result the rigid local structure and coplanar conformation between 5-methoxy group and base that is caused by hydrogen-bond interaction. the A-DNA the researchers had synthesized had similar features of RNA and it had high diffraction quality. Hydrogen-bond formation between Omethyl hydrogen and ribosyl phosphate oxygen in 5-methoxyuridine was found for the first time and this was confirmed by the UV melting point determination experiment. Significant Findings.melting point determination to compare melting temperatures that determine the strength of base pairing through hydrogen-bonding. Furthermore. After determining the measurements required for the parameters in crystallographic data. Firstly.

. (2003) Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons.A. Harris.Z. E. K. (2010) Selenium derivatization of nucleic acids for X-ray crystalstructure and function studies. T.. J.....S. Pan. J. Vendeix. Cantara.H.S.A. 39. 447.. D195–D201. 6383–6391.K... Fabris. Hosono.F. The Royal Society of Chemistry. D. Cell 149. Lett. 7. FEBS Lett. and Williams. M. 202-2013.J. M..J. 7 49–752.J.. J. Loakes. (2006) Nucleic Acids in Chemistry and Biology 3e. 1–4. (1999) A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell-free translation system. M.).D. Sheng. Org. Okumura.. RNAMDB: 201 1 update.. Y okoyama. 9. K. Takai. and Takaku. and de Pouplana. (2007) Synthesis of a 2'-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study.Z. D. Jiang. Pavon-Eternod. (Eds. Nucleic Acids Res. Biodivers.S. Crain..F. Salon. (201 1) The RNA modification database.F. Novoa.. Chem. Zhang. M.. M. Takai.P. L.X. G. 753–785. McCloskey.. and Y okoyama... UK.A.. Rozenski. and Agris. (2012) A role for tRNA modifications in genome structure and codon usage. W.. and Huang.A. Gait.J.K. 3 1.References Blackburn. and Huang. Cambridge.P. Sheng. . Nucleic Acids Res. R. 1.

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