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Nucleic Acids
Understanding RNA/DNA fold and function is of profound importance
The information in genes is coded in the form of DNA whereas RNA is used to decode this information and use it to direct protein synthesis. Thus understanding the nucleic acid (DNA and RNA) fold and function is of profound importance. The two methods for oligonucleotide structure determination are X-ray crystallography and NMR spectroscopy. Contrary to protein structure determination, these two methods contribute almost equal numbers to the nucleic acid structures. Today the investigations of oligonucleotides reach out to ever larger structures and complexes. This has become possible thanks to intensive development of multidimensional NMR methods and advances in the isotope labelling techniques of nucleic acids. Another key factor is the hardware development of NMR, such as the availability of ever higher magnetic fields and high sensitivity CryoProbes.
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The NMR structure determination of RNA and DNA fragments is complicated by a strong overlap of the NMR signals. This is because these biomacromolecules are built of only 4 different subunits, the nucleotides, whereas protein sequences consist of 20 natural amino acids. In addition, the oligonucleotides are often found in helical stuctures, whereas in native protein folds the variation is larger.
Two triple resonance CryoProbes are of particular interest with regard to NMR of labelled oligonucleotides. First, the TCI CryoProbe that can be used to correlate proton and carbon to nitrogen in the nucleobases. Second, the TCI-HPC CryoProbe that can be use to correlate proton and carbon to phosphorus, thus enabling the tracking of the nucleic acid sequence over connecting phosphodiester links. In addition, our TopSpin software package provides a comprehensive and ready-to-use set of the latest NMR experiments for investigation of nucleic acids.
Recently 13C-detection has become an option for nucleic acids as suitable CryoProbes have become available. The spectra (above) displays the carbon-carbon and carbon-nitrogen correlated spectra of a 13C, 15N labelled 14-mer RNA hairpin. The RNA sequence is displayed in the oval with color-coding corresponding to that of the nucleobase frequencies in the spectra.
Ref: H. Kovacs, D. Moskau, M. Spraul, Prog. NMR Spectroscopy 46 (2005) 131-155