Monomers for oligonucleotide synthesis with linkers carrying reactive residues: II. Synthesis of phosphoamidites based of uridine and cytosine and containing a linker with methoxyoxalamide groups in position 2'

A convenient preparative synthesis of 2'-amino-2'-deoxyuridine was developed. Starting from 2'-amino-2'-deoxyuridine and 2'-amino-2'-deoxycytidine, monomers for the phosphoamidite oligonucleotide synthesis were obtained that carry a linker with methoxyoxalamide groups in position 2'. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 3; see also http://www.maik.ru.     

4-aminometyl-3-nitrobenzoic acid--a photocleavable linker for oligonucleotides containing combinatorial libraries

We detail the design, synthesis, and characterization of an o-nitrobenzyl-based photolabile linker containing amine and carboxyl anchor groups. A model nucleoside monomer modified with an imidazole residue and a precursor unit linked to a heterocyclic base through a photolabile tether is constructed Upon UV irradiation (313- 365 nm), the imidazole containing part of this molecule is released.     

Frequency of the 735G → A mutation of the 5′-splice donor site of intron 14 of the dihydropyrimidine dehydrogenase gene (<Emphasis Type="Italic">DPYD</Emphasis>) in residents of novosibirsk region (Russia) as revealed with fluorescent oligonucleotides

A simple method was developed for end-point fluorescence detection of the 735G → A mutation of the 5′-splice donor site of intron 14 of the dihidropyrimidine dehydrogenase gene (DPYD). The method was based on allele-specific PCR with duplex Scorpion primers. The genotyping results obtained by the fluorescent end-point PCR technique completely coincided with the results obtained by allele-specific PCR with amplicon detection in agarose gel. Genotyping was performed in 291 DNA samples from residents of Novosibirsk region (Russia), and two heterozygotes (0.69%) were detected.     

Biotin-decorated anti-cancer nucleotide theranostic conjugate of human serum albumin: Where the seed meets the soil?

Human serum albumin is playing an increasing role as a drug carrier in clinical settings. Biotin molecules are often used as suitable tags in targeted anti-tumor drug delivery systems. We report on the synthesis and properties of a new multimodal theranostic conjugate based on an anti-cancer fluorinated nucleotide conjugated with a biotinylated dual-labeled albumin. Interestingly, in vitro and in vivo study revealed stronger anti-tumor activity of the non-tagged theranostic conjugate than that of the biotin-tagged conjugate, which can be explained by decreased binding of the biotin-tagged conjugate to cellular receptors. Our study sheds light on the importance of site-specific albumin modification for the design of albumin-based drugs with desirable pharmaceutical properties.     

Synthetic constructs functionally mimicking ribonuclease A

The mechanism of hydrolysis of RNA substrates—diribonucleoside monophosphate CpA and decaribonucleotide UUCAUGUAAA—by chemical constructs functionally mimicking ribonuclease A was studied. It is shown that RNA cleavage by chemical RNases 2L2 and 2D3 proceeds similar to the RNase A-induced RNA hydrolysis through 2′,3′-cyclophosphate as an intermediate product. A comparison of hydrolyses of CpA in water and D₂O revealed an isotope effect (K _H/K _D=2.28), which implies acid-base catalysis at the limiting stage of the reaction. Two feasible mechanisms of RNA hydrolysis by chemical RNases (linear and adjacent) are discussed.     

Synthesis and high stability of complementary complexes of N-(2-hydroxyethyl)phenazinium derivatives of oligonucleotides.

Two simple methods for the synthesis of oligonucleotides bearing a N-(2-hydroxyethyl)phenazinium (Phn) residue at the 5'- and/or 3'-terminal phosphate groups are proposed. By forming complexes between a dodecanucleotide d(pApApCpCpTpGpTpTpTpGpGpC), a heptanucleotide d(pCpCpApApApCpA), and Phn derivatives of the latter, it is shown that the introduction of a dye at the end of an oligonucleotide chain strongly stabilizes its complementary complexes. The Tmax and the thermodynamic parameters (delta H, delta S, delta G) of complex formation were determined. According to these data, coupling of a dye with the 5'-terminal phosphate group is the most advantageous: delta G(37 degrees C) is increased by 3.59 +/- 0.04 kcal/mol compared to 2.06 +/- 0.04 kcal/mol for 3'-Phn derivatives. The elongation of the linker, which connects the dye to the oligonucleotide, from a dimethylene up to a heptamethylene usually leads to destabilization of the oligonucleotide complex. The complementary complex formed by the 3',5'-di-Phn derivative of the heptanucleotide was found to be the most stable among all duplexes investigated. Relative to the unmodified complex the increase in free energy was 4.96 +/- 0.04 kcal/mol. The association constant of this modified complex at 37 degrees C is 9.5 x 10(6) M-1, whereas the analogous value for the unmodified complex is only 3 x 10(3) M-1.     

Molecular design of artificial ribonucleases using electrostatic interaction

A number of small organic ribonucleases have been synthesized with rigid polycationic structures containing an aromatic framework with two residues of bis-quaternary salts of 1,4-diazabicyclo[2.2.2]octane (DABCO) bearing various substituents. The compounds carrying positively charged groups connected via rigid linker are expected to bend the sugar-phosphate backbone and can stimulate the intramolecular phosphoester transfer reaction.     

Toward the development of metal-free synthetic nucleases: cleavage of a model substrates by 1,4-diazabicyclo[2.2.2]octane derivatives

Artificial ribonucleases of A(n)BCL series were synthesized by solid-phase method. They consist of a hydrophobic alkyl radical A (n = 3-12 carbon atoms), an "RNA-binding domain" B (bisquaternary salt of 1,4-diazabicyclo[2.2.2]octane), a "catalytic domain" C (histidine residue) and a "linker" L that joins the domains B and C. The effect of the alkyl radical on the catalytic properties of the chemical catalyst was studied using three activated phosphate ester substrates: p-nitrophenyl phosphate, bis-p-nitrophenyl phosphate, and thymidine-3'-p-nitrophenyl phosphate.     

Design and synthesis of metal-free artificial ribonucleases

The present review is aimed at giving a general overview of our results in the field of designing and synthesizing simple peptide-like molecules that mimic structural and functional aspects of natural ribonucleases, as well as designing oligonucleotide-based artificial ribonucleases.     

Artificial ribonucleases: from combinatorial libraries to efficient catalysts of RNA cleavage

Combinatorial libraries of small organic compounds capable of cleaving RNA were synthesized. The compounds contain benzene ring substituted with two residues of bis quaternary salt of diazabicyclo[2.2.2]octane (DABCO) bearing hydrophobic fragments of different length and structure, attached to DABCO at the bridge position. These compounds, lacking traditional functionalities involved in transesterification reaction, exhibit pronounced RNA cleavage activity. To identify the most active artificial ribonucleases, sublibraries and truncated libraries, containing compounds lacking one of substituents were synthesized. Analysis of ribonuclease activity of truncated libraries resulted in identification of the most active compounds, which are characterized by the presence of at least one long oligomethylene substituent.