Synthesis and properties of GuNA purine/pyrimidine nucleosides and oligonucleotides

Facile synthesis of GuNA (guanidine-bridged nucleic acid) phosphoramidites bearing thymine, adenine, guanine, and 5-methylcytosine nucleobases and a robust method for the preparation of GuNA-modified oligonucleotides are described.

Three thymine/adenine binding modes of the ruthenium complex Λ-[Ru(TAP)2(dppz)]2+ to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography

Λ-[Ru(TAP)2(dppz)]2+ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT).

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

Fluorescent pyrene–linker–nucleobase (nucleobase = thymine, adenine) conjugates with carbonyl and hydroxy functionalities in the linker were synthesized and characterized. X-ray single-crystal structure analysis performed for the pyrene–C(O)CH2CH2–thymine (2) conjugate reveals dimers of molecules 2 stabilized by hydrogen bonds between the thymine moieties. The photochemical characterization showed structure-dependent fluorescence properties of the investigated compounds. The conjugates bearing a carbonyl function represent weak emitters as compared to compounds with a hydroxy function in the linker. The self-assembly properties of pyrene nucleobases were investigated in respect to their binding to single and double strand oligonucleotides in water and in buffer solution. In respect to the complementary oligothymidine T10 template in water, compounds 3 and 5 both show a self-assembling behavior according to canonical base–base pairing. However, in buffer solution, derivative 5 was much more effective than 3 in binding to the T10 template. Furthermore the adenine derivative 5 binds to the double-stranded (dA)10–T10 template with a self-assembly ratio of 112%. Such a high value of a self-assembly ratio can be rationalized by a triple-helix-like binding, intercalation, or a mixture of both. Remarkably, compound 5 also shows dual staining pattern in living HeLa cells. Confocal microscopy confirmed that 5 predominantly stains mitochondria but it also accumulates in the nucleoli of the cells.

Cooperative hydrogen-bonding of the adenine–thymine pair as a strategy for lowering the limit of detection of thymine by surface-enhanced Raman spectroscopy

The formation of cooperative hydrogen bonds between the thymine–adenine pair was used to indirectly determine thymine by SERS, improving the limit of detection values up to two orders of magnitude.