In addition to a well known right handed B form double helix, DNA molecules can form higher order structures such as G-quadruplexes. Oligonucleotide sequences rich in guanine nucleotides can form such unusual structures in the presence of certain cations, such as K+ or Na+. The formation of G-quadruplexes is closely related to human diseases. Guanine-rich sequences can in an environment almost completely free of G-quadruplex promoting cations form well defined structures, which can be considered as an intermediates on the way to folding into G-quadruplexes. It is interesting to note that the guanine bases are not held together by Hoogsteen hydrogen bonds like in G-quartets but rather by alternative base pairing.
B.04 Guest lectureCOBISS.SI-ID: 5922074
In the scope of the invited lecture I have also showen the determination of structures of nucleic acids rich in guanine residues using NMR spectroscopy and complementary methods. NMR spectroscopy can monitor the formation of such structures. In certain cases, folding in the presence of cations is carried out from well-defined structures.
B.04 Guest lectureCOBISS.SI-ID: 5930266
We made a patent application, where we have developed a method for the characterization of guanine residues which are included in the base pairs within pre-folded structures of oligonucleotides in solution using selective replacement of a single guanine with nebularine residue. The above process is based on the selective introduction of one nebularine residue instead of guanine residue in the oligonucleotide sequence. Since the nebularine lacks a carbonyl group on C6 atom and amino NH2 group, NH imino protons cannot be involved in GG N1-carbonyl base pair. This base pair is crucial in stabilization of pre-folded structures. The method for determination of the participation of guanine residues in GG N1-carbonyl base pairs is based on the difference in the number and the chemical shifts of aromatic protons of nebularine and guanine residues. Nebularine has three aromatic protons, which are downfiled in the 1H NMR spectrum in comparison to aromatic proton of the guanine residue. In the case that, more than three signals in the 1H NMR spectrum are present for aromatic protons of nebularine residue, the guanine residue at this position within the oligonucleotide has been involved in base pair. In the case if only three signals for aromatic protons of nebularine residue would be observed, guanine residue at this position within the oligonucleotide is not crucial for stabilization of pre-folded structure.
F.33 Slovenian patentCOBISS.SI-ID: 6077210