A novel versatile phosphoramidite building block for the synthesis of 5'- and 3'-hydrazide modified oligonucleotides

We introduce a novel versatile phosphoramidite building block for the modification of oligonucleotides (ONs) with acyl hydrazides on the 5'- or 3'-terminus, or both. The reaction of these hydrazide functionalized ONs with 4-methoxyphenylaldehyde is demonstrated for solution derivatization. Hydrazides are considered nowadays as promising reactants, which show enhanced reactivity at neutral and slightly acidic conditions and higher stability of yielding products as compared to the aliphatic amines, which are broadly used for ONs derivatization. Our method to introduce hydrazides into ONs employs a phosphoramidite modifier designed to split, during ammonia or lithium hydroxide treatment, into two hydrazides via beta-elimination of a central bis-2-carbonylethoxysulfone unit. It allows the creation of ONs derivatized with a hydrazide moiety at the 5'-, 3'- and both 5'- and 3'-termini, as well as two different hydrazide containing ONs at the same time, viz. in one sequence on the same solid support In latter case one can, for example, synthesize two hydrazide containing ONs, where one is 5'-modified and second one is 3'-modified.     

A Novel Versatile Phosphoramidite Building Block for the Synthesis of 5′- and 3′-Hydrazide Modified Oligonucleotides

We introduce a novel versatile phosphoramidite building block for the modification of oligonucleotides (ONs) with acyl hydrazides on the 5′- or 3′-terminus, or both. The reaction of these hydrazide functionalized ONs with 4-methoxyphenylaldehyde is demonstrated for solution derivatization. Hydrazides are considered nowadays as promising reactants, which show enhanced reactivity at neutral and slightly acidic conditions and higher stability of yielding products as compared to the aliphatic amines, which are broadly used for ONs derivatization.

Our method to introduce hydrazides into ONs employs a phosphoramidite modifier designed to split, during ammonia or lithium hydroxide treatment, into two hydrazides via β-elimination of a central bis-2-carbonylethoxysulfone unit. It allows the creation of ONs derivatized with a hydrazide moiety at the 5′-, 3′- and both 5′- and 3′-termini, as well as two different hydrazide containing ONs at the same time, viz. in one sequence on the same solid support. In latter case one can, for example, synthesize two hydrazide containing ONs, where one is 5′-modified and second one is 3′-modified.     

Synthesis and hybridization properties of oligonucleotides containing 2'-O-modified ribonucleotides.

A versatile, general way is described for the introduction of different functional groups into oligonucleotides by means of a simple linker at the 2'-position of the sugar. Nucleotide building blocks carrying lipophilic, intercalating or tertiary amino groups can be placed deliberately at any desired position of oligonucleotides by standard automated oligonucleotide synthesis. Thermal denaturation studies with these oligonucleotides reveal the following general trends: i) Modification with lipophilic n-octyl groups has little if any effect on duplex stability; a destabilizing (lipophilic) substituent is better tolerated at or near the ends than in the middle of the oligo. ii) An intercalating substituent (2-aminoanthraquinone) substantially increases duplex stability. iii) N,N-Dimethyl amino residues also increase duplex stability though to a smaller extent than intercalating residues. iv) Modifications at the 5'-end have a more pronounced influence on the TM than the corresponding 3'-modifications. v) Oligonucleotides modified in such a way show little or no loss in sequence specificity.     

Synthesis of Monomers Bearing at the 2′‐Position Cyanomethoxycarbonyl Group for Phosphoramidite Oligonucleotide Synthesis

A novel series of phosphoroamidites for the synthesis of 2′‐modified oligonucleotides was designed and synthesized on the base of 2′‐amino uridine and 2′‐amino arabinoadenosine. The amino groups in these compounds were acidified by bis‐cyanomethyl esters of different dicarbonic acids. Generated reactive linker groups containing cyanomethoxycarbonyl groups are stable under conditions of oligonucleotide synthesis but could be easily functionalised in post‐synthetic stage by treatment with compounds bearing primary amino groups.     

Combinatorial Library of Artificial Ribonucleases

Abstract

Conjugates of lanthanide complexes and oligonucleotides have been shown to bind and to cleave complementary RNA. Modified oligonucleotide building blocks are required to ensure stability of the oligonucleotide against cellular nucleases. For an efficient cleavage, an accessible site on the structured mRNA is required. For the identification of active oligoribonucleotide-lanthanide complex conjugates, we have used a combinatorial library of conjugate sequences.     

A New Protecting Group Strategy for Amino Groups in Oligonucleotide Chemistry: CEOC Group

Abstract

A new protecting group, 2-cyanoethyloxycarbonyl, or CEOC, has been developed for amino groups and utilized in synthesizing modified oligonucleotides. (CEOC)-oxy-succinimide reagent has been synthesized to introduce this protecting group. The protecting group is removed by standard oligonucleotide deprotection protocols. Using this approach, oligonucleotides have been synthesized with various types of alkylamine substituents.     

Synthesis and use of labelled nucleoside phosphoramidite building blocks bearing a reporter group: biotinyl, dinitrophenyl, pyrenyl and dansyl.

The synthesis of protected nucleoside phosphoramidites bearing various markers such as biotinyl, dinitrophenyl, dansyl and pyrenyl groups are reported. These labelled deoxynucleosides phosphoramidites were used for solid phase oligonucleotide synthesis in the same way than the usual protected phosphoramidities without any change in the synthetic cycle and the deprotection step. The new labelled building blocks described herein have been used in conjunction with the labile base protected phosphoramidites ('PAC phosphoramidites') which allowed mild ammonia deprotection, especially recommended for the dinitrophenyl-labelled oligonucleotides. Multiple labelling (i.e. 10 to 20 biotins) can be efficiently and easily performed, on the same oligonucleotide which results in an increase of sensitivity. The polylabelled oligonucleotides are chemically well defined and gave increased signal and low background coloration for in situ hybridisation. The modified oligonucleotides can still be kinased in the normal way as the reporter groups are on the heterocycles.     

Discovery of histone deacetylase 8 selective inhibitors

We have developed an efficient method for synthesizing candidate histone deacetylase (HDAC) inhibitors in 96-well plates, which are used directly in high-throughput screening. We selected building blocks having hydrazide, aldehyde and hydroxamic acid functionalities. The hydrazides were coupled with different aldehydes in DMSO. The resulting products have the previously identified ‘cap/linker/biasing element’ structure known to favor inhibition of HDACs. These compounds were assayed without further purification. HDAC8-selective inhibitors were discovered from this novel collection of compounds.     

Synthesis of 3'-3'-linked oligonucleotides branched by a pentaerythritol linker and the thermal stabilities of the triplexes with single-stranded DNA or RNA

Synthesis of 3'-3'-linked oligonucleotides branched by a pentaerythritol linker is described. The branched oligonucleotides were synthesized on a DNA/RNA synthesizer using a controlled pore glass (CPG) with a pentaerythritol linker carrying 4,4'-dimethoxytrityl (DMTr) and levulinyl (Lev) groups. The stability of the triplexes between the branched oligonucleotides and the target single-stranded DNA or RNA was studied by thermal denaturation. The oligonucleotides with the pentaerythritol linker formed thermally stable triplexes with the single-stranded DNA and RNA. Furthermore, the branched oligonucleotides containing 2'-O-methylribonucleosides, especially the oligonucleotide composed of 2'-deoxyribonucleosides and 2'-O-methylribonucleosides, stabilized the triplexes with the single-stranded DNA or RNA. Thus, the branched oligonucleotide containing 2'-O-methylribonucleosides may be a candidate for a novel antisense molecule by the triplex formation.     

Spectrophotometric determination of hydrazine, hydrazides, and their mixtures with trinitrobenzenesulfonic acid

A method has been developed to measure hydrazine, hydrazides, and their mixtures using a modification of the trinitrobenzenesulfonic acid method [T. Okuyama and K. Satake (1960) J. Biochem. (Tokyo) 47, 654-660]. After incubation of the sample containing hydrazine and hydrazide with trinitrobenzenesulfonate at pH 8.5 at room temperature for 40 min, the reaction mixture was diluted with a Na2CO3-NaHCO3 buffer (0.1 M, pH 10.8) rather than with 0.5 M HCl. Different chromogens were produced from the reaction of hydrazine (lambda max = 570 nm) and hydrazides (lambda max = 385 and 500 nm) with trinitrobenzenesulfonic acid. The method allowed simultaneous determination of hydrazine (5 to 60 nmol) with hydrazide (10 to 120 nmol) in a mixture with a standard deviation of less than 5%. The presence of amino compounds (except for amino sugars) did not interfere with the measurement of hydrazine or hydrazides. Interference by amino sugars in the determination of hydrazine or hydrazides was eliminated by pretreatment of the sample with NaBH4 to reduce the amino sugars to 2-amino-2-deoxy-hexitols.     

Interactions between amino acids and nucleotides in the prebiotic milieu

In the study of chemical evolution we are interested in the path by which nucleic acids and proteins may have arisen under prebiotic conditions giving rise to those interactions which are generally postulated for the threshold of life. Although laboratory experiments have demonstrated that most of the building blocks of life can be generated from the raw material of the primitive atmosphere, in the genesis of polymers, however, the efforts have been less conclusive. It is reasonable to suppose that small peptides and small oligonucleotides may have interacted in the ‘primordial soup’ giving rise to the earliest association between nucleic acids and proteins. The beginnings of these processes could be related to the properties of individual amino acids and nucleotides. The interaction of oligomers with amino acids has been studied by the use of ion exchange and NMR spectroscopy. The observed affinities appear to depend on the given amino acid and the oligonucleotide chain length. The results so far suggest that direct amino-acid nucleotide interactions could have made a contribution to the early evolution of the Genetic Code.     

New Hydrazides and Hydrazide‐Hydrazones of 2,3‐Dihalogen Substituted Propionic Acids: Synthesis and in vitro Antimicrobial Activity Evaluation

The main aim of this research was the synthesis, spectral identification and in vitro antimicrobial evaluation of new hydrazides and hydrazide‐hydrazones of 2,3‐dihalogen substituted propionic acids. New hydrazides were obtained by the substitution reaction of appropriate ethyl esters of 2,3‐dihalogen substituted propionic acids with hydrazine hydrate. Then obtained hydrazides were subjected to condensation reaction with various aldehydes which yielded with new hydrazide‐hydrazone derivatives. All obtained compounds were identified on the basis of spectral methods (¹H‐NMR, ¹³C‐NMR) and in vitro screened against a panel of bacterial and fungal strains according to EUCAST and CLSI guidelines.     

Surprising duplex stabilisation upon mismatch introduction within triply modified duplexes

Three different modified phosphoramidite nucleoside building blocks equipped with additional protected imidazole, masked alcohol and masked carboxylate functionality are synthesized and incorporated into oligonucleotides. Based on the serine-protease active site model, doubly and triply modified duplexes are created and tested for stability. Analysis of different spatial distributions of the extra functionalities shows that careful positioning can even overcome duplex destabilisation caused by the introduction of mismatches.     

Hydrazide derivatives produce active oxygen species as hydrazine

It is well documented that some hydrazines are quite sensitive to oxidation and may serve as the electron donor for the reduction of oxygen, whereas hydrazides are not believed to react directly with oxygen. Data presented in this paper show that both hydrazides and hydrazines share an N-N moiety, which is assumed to react with atmospheric oxygen and produce oxygen radicals, at various degrees of efficiency. Since spectrometric measurements of hydrazide just after solubilization showed that the molecular mass remains constant in the absence of oxygen, we can conclude that hydrazides do not react with the oxygen through a slow spontaneous hydrolytic release of hydrazine. However, hydrazine is more reactive than hydrazide, which requires hours rather than minutes to produce measurable quantities of radical species. Differences were also apparent for various substituted derivatives. The reaction was significantly enhanced by the presence of metal ions. Data reported here demonstrate that hydrazides cause irreversible damage to the prosthetic group of proteins as well as causing degradation of the polypeptide chain into small fragments.     

Alpha-hydroxybenzylphosphonate modified oligonucleotides: synthesis, properties, and a novel route via monomer building blocks

In general, alpha-hydroxybenzylphosphonate modified 2'-deoxyadenosine-thymidine dimer building blocks 1, 2 are utilized for the incorporation into alpha-hydroxybenzylphosphonate pro-oligonucleotides. For a universal application of our pro-oligonucleotide concept on biologically relevant oligonucleotides a route for the synthesis of modified monomer building blocks 3 was developed and is presented herein.     

DNA or RNA oligonucleotide 2'-hydrazides for chemoselective click-type ligation with carbonyl compounds

An efficient method for the synthesis of DNA or RNA oligonucleotide 2'-hydrazides is described. Fully deprotected oligonucleotides containing a hydrazide group at the 2'-position of a uridine residue were obtained by a novel two-step procedure: periodate cleavage of an oligonucleotide with 1,2-diol group followed by conversion of the aldehyde to hydrazide with an extended linker arm using a homobifunctional reagent succinic dihydrazide and NaBH(3)CN. The resulting oligonucleotide 2'-hydrazides were efficiently conjugated by a click-type reaction at acidic pH to aliphatic or aromatic aldehydes with or without NaBH(3)CN reduction to afford novel 2'-conjugates.     

Synthesis of DNA oligonucleotides containing 5-(mercaptomethyl)-2'-deoxyuridine moieties

Recently thiolated oligonucleotides have attracted significant interest due to their ability to efficiently undergo stable bond formation with gold nanoparticles and surfaces to form DNA conjugates. In this respect we became interested in the synthesis of oligonucleotides that bear short thioalkyl functions located at the nucleobase. Here we present a strategy for the synthesis of DNA oligonucleotides that bear 5-(mercaptomethyl)-2'-deoxyuridine moieties. The building blocks were synthesized in a straightforward manner from thymidine. Only moderate changes of standard protocols for automated DNA synthesis are required for the generation of modified oligonucleotides containing the thiolated building blocks.     

DNA or RNA Oligonucleotide 2′-Hydrazides for Chemoselective Click-Type Ligation with Carbonyl Compounds

An efficient method for the synthesis of DNA or RNA oligonucleotide 2′-hydrazides is described. Fully deprotected oligonucleotides containing a hydrazide group at the 2′-position of a uridine residue were obtained by a novel two-step procedure: periodate cleavage of an oligonucleotide with 1,2-diol group followed by conversion of the aldehyde to hydrazide with an extended linker arm using a homobifunctional reagent succinic dihydrazide and NaBH₃CN. The resulting oligonucleotide 2′-hydrazides were efficiently conjugated by a click-type reaction at acidic pH to aliphatic or aromatic aldehydes with or without NaBH₃CN reduction to afford novel 2′-conjugates.     

Synthesis of monomers bearing at the 2'-position cyanomethoxycarbonyl group for phosphoramidite oligonucleotide synthesis

A novel series of phosphoroamidites for the synthesis of 2-modified oligonucleotides was designed and synthesized on the base of 2'-amino uridine and 2'-amino arabinoadenosine. The amino groups in these compounds were acidified by bis-cyanomethyl esters of different dicarbonic acids. Generated reactive linker groups containing cyanomethoxycarbonyl groups are stable under conditions of oligonucleotide synthesis but could be easily functionalised in post-synthetic stage by treatment with compounds bearing primary amino groups.