3′-Deoxy-2′-phosphoramidites of adenosine and 5-methyluridine used for the solid phase synthesis of unnatural 3′-deoxy-2′–5″-Oligonucleotides

Neuroprotective potential of adenosine A1 receptor partial agonists in experimental models of cerebral ischemia

Cerebral ischemia is the second most common cause of death and a major cause of disability worldwide. Available therapies are based only on anticoagulants or recombinant tissue plasminogen activator. Extracellular adenosine increases during ischemia and acts as a neuroprotective endogenous agent mainly by activating adenosine A₁ receptors (A₁ Rs) which control calcium influx, glutamate release, membrane potential, and metabolism. Accordingly, in many experimental paradigms it has been already demonstrated that the stimulation of A₁ R with full agonists is able to reduce ischemia-related structural and functional brain damage; unfortunately, cardiovascular side effects and desensitization of A₁ R induced by these compounds have strongly limited their exploitation in stroke therapy so far. Among the newly emerging compounds, A₁ R partial agonists could be almost free of side effects and equally effective. Therefore, we decided to evaluate the neuroprotective potential of two A₁ R partial agonists, namely 2'-dCCPA and 3'-dCCPA, in in vitro and ex vivo experimental models of cerebral ischemia. Within the experimental paradigm of oxygen-glucose deprivation in vitro in human neuroblastoma (SH-SY5Y) cells both A₁ R partial agonists increased cell viability. Considering the high level of expression of A₁ Rs in the hippocampus and the susceptibility of CA1 region to hypoxia, we performed electrophysiological experiments in this subfield. The application of 7 min of oxygen-glucose deprivation constantly produces an irreversible synaptic failure in all the C57Bl/6 mice hippocampal slices evaluated; both tested compounds allowed a significant recovery of synaptic transmission. These findings demonstrate that A₁ R and its partial agonists are still of interest for cerebral ischemia therapy. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.

Synthesis and hybridizing properties of isoDNAs including 3'-O,4'-C-ethyleneoxy-bridged 5-methyluridine derivatives

3',4'-Ethyleneoxy-bridged 5-methyluridine derivatives with methyl groups in the bridge, (R)-Me-3',4'-EoNA-T and (S)-Me-3',4'-EoNA-T, were synthesized, and these two analogs and unsubstituted 3',4'-EoNA-T were successfully incorporated into a 2',5'-linked oligonucleotide (isoDNA). Their duplex-forming ability with complementary DNA and complementary RNA, and triplex-forming ability with double-stranded DNA, were evaluated by UV-melting experiments. The results indicated that isoDNAs, including these 3',4'-EoNA analogs, could hybridize exclusively with complementary RNA. In particular, 3',4'-EoNA-T and (R)-Me-3',4'-EoNA-T modifications within isoDNA could stabilize the duplexes with complementary RNA compared with unmodified or 3',4'-BNA-modified isoDNAs.

Cleavage of oligonucleotides containing a P3'→N5' phosphoramidate linkage mediated by single-stranded oligonucleotide templates

Double-stranded DNA (dsDNA) templates can hybridize to and accelerate cleavage of oligonucleotides containing a P3'→N5' phosphoramidate (P-N) linkage. This dsDNA-templated cleavage of P-N linkages could be due to conformational strain placed on the linkage upon triplex formation. To determine whether duplex formation also induced conformational strain, we examined the reactivity of the oligonucleotides with a P-N linkage in the presence of single-stranded templates, and compared these reactions to those with dsDNA templates. P-N oligonucleotides that are cleaved upon duplex formation could be used as probes to detect single-stranded nucleic acids.

Presence of 2',5'-linkages in a homopyrimidine DNA oligonucleotide promotes stable triplex formation under physiological conditions

We prepared 15-mer homopyrimidine oligonucleotides containing three or four 2',5'-linked DNA units, and their ability as a triplex-forming oligonucleotide (TFO) was analyzed in detail UV melting experiments showed that replacement of a 3',5'-linkage by a 2',5'-linkage at every third or fourth residue in TFO significantly promoted stable triplex formation under physiological conditions.

Promotion of stable triplex formation by partial incorporation of 2',5'-phosphodiester linkages into triplex-forming oligonucleotides

Pentadecamer homopyrimidine oligonucleotides containing three or more 2',5'-phosphodiester linkages in different modes were prepared and used to evaluate the ability as a triplex-forming oligonucleotide (TFO), and it was found that discontinuous replacement of the 3',5'-phosphodiester linkages in TFO by 2',5'-linkages significantly stabilizes parallel-motif triplexes.

Nucleosidyl-O-Methylphosphonates: a pool of monomers for modified oligonucleotides

An unique set of 5'-O- and 3'-O-phosphonomethyl derivatives of four natural 2'-deoxyribonucleosides, 1-(2-deoxy-beta-D-threo-pentofuranosyl)thymine, 5'-O- and 2'-O-phosphonomethyl derivatives of 1-(3-deoxy-beta-D-erythro-pentofuranosyl)thymine, and 1-(3-deoxy-beta-D-threo-pentofuranosyl)thymine, has been synthesized as a pool of monomers for the synthesis of modified oligonucleotides. The phosphonate moiety was protected with 4-methoxy-1-oxido-2-pyridylmethyl ester group, serving also as an intramolecular catalyst in the coupling step.

Effect of 2'-5' phosphodiesters on DNA transesterification by vaccinia topoisomerase

Vaccinia topoisomerase forms a covalent DNA-(3'-phosphotyrosyl)-enzyme intermediate at a pentapyrimidine target site 5'-CCCTTp downward arrow in duplex DNA. By introducing single 2'-5' phosphodiesters in lieu of a standard 3'-5' phosphodiester linkage, we illuminate the contributions of phosphodiester connectivity to DNA transesterification. We find that the DNA cleavage reaction was slowed by more than six orders of magnitude when a 2'-5' linkage was present at the scissile phosphodiester (CCCTT(2')p downward arrow(5')A). Thus, vaccinia topoisomerase is unable to form a DNA-(2'-phosphotyrosyl)-enzyme intermediate. We hypothesize that the altered geometry of the 2'-5' phosphodiester limits the ability of the tyrosine nucleophile to attain a requisite, presumably apical orientation with respect to the 5'-OH leaving group. A 2'-5' phosphodiester located to the 3' side of the cleavage site (CCCTTp downward arrowN(2')p(5')N) reduced the rate of transesterification by a factor of 500. In contrast, 2'-5' phosphodiesters at four other sites in the scissile strand (TpCGCCCTpT downward arrowATpTpC) and five positions in the nonscissile strand (3'-GGGpApApTpApA) had no effect on transesterification rate. The DNAs containing 2'-5' phosphodiesters were protected from digestion by exonuclease III. We found that exonuclease III was consistently arrested at positions 1 and 2 nucleotides prior to the encounter of its active site with the modified 2'-5' phosphodiester and that the 2'-5' linkage itself was poorly hydrolyzed by exonuclease III.

Probing structure and function with alternative nucleic acids bearing 2',5'-linked, zwitterionic, and isocytosine-isoguanine components

The incorporation of alternative functional components into nucleic acids can provide insight into what molecular features are necessary for an informational macromolecule to be successful. It can also provide a means to improve particular physical characteristics of nucleic acids for diagnostic and therapeutic purposes, or probe mechanisms. By testing the fitness of nucleic acid-like molecules derived by structural permutations of RNA, it may also prove possible to trace a path from simple prebiotic precursors to biotic molecules. This article describes the applications of 2',5'-phosphodiester linked, zwitterionic, and base-permuted nucleic acid derivatives.

Stereocontrolled syntheses of deoxyribonucleosides via photoinduced electron-transfer deoxygenation of benzoyl-protected ribo- and arabinonucleosides

The stereocontrolled, de novo syntheses of beta-2'-deoxy-, alpha-2'-deoxy-, beta-3'-deoxy-, and beta-2', 3'-dideoxyribonucleosides are described. Strategically protected ribose, arabinose, and xylose glycosylation precursors were synthesized bearing C2-esters capable of directing Vorbrüggen glycosylation. The key step is the regioselective deoxygenation of the desired hydroxyl group as either the benzoyl- or 3-(trifluoromethyl)benzoyl derivative. This deoxygenation is accomplished via a photoinduced electron-transfer (PET) mechanism using carbazole derivatives as the photosensitizer. The syntheses of the desired deoxynucleoside generally proceed in three steps from a common, readily available precursor.

DNA duplexes containing 3'-deoxynucleotides as substrates for DNA topoisomerase I cleavage and ligation

The DNA cleavage-ligation reaction of DNA topoisomerase I was investigated employing synthetic DNA substrates containing 3'-deoxyadenosine or 3'-deoxythymidine at specific sites and acceptor oligonucleotides of different lengths. The modified nucleotides were substituted systematically within the putative enzyme-binding domain and also next to the high efficiency cleavage site to determine the effect of single base changes on enzyme function. Depending on the site of substitution, the facility of the cleavage and ligation reactions were altered. The bases at positions -1 and -2 on the noncleaved strand were found to be important for determining the site of cleavage. Inclusion of 3'-deoxythymidine in the scissile strand at position -1 permitted the demonstration that topoisomerase I can cleave and form a 2' --> 5'-phosphodiester linkage. Partial duplexes doubly modified at positions -4 or -6 in the noncleaved strand and at positions +1 or -1 within scissile strand were not good substrates for topoisomerase I, showing that cleavage can depend importantly on binding interactions based on structural alterations at spatially separated sites. Substitution of a 3'-deoxynucleotide on the scissile strand at position -6 enhanced formation of the ligation product resulting from cleavage at site 1 and suppressed cleavage at site 2.

(2'-5')-Oligo-3'-deoxynucleotides: selective binding to single-stranded RNA but not DNA

Oligodeoxynucleotides with (2'-5') internucleotide linkages have been synthesized on a solid support via standard cyanoethyl phosphoramidite chemistry. This simple change in the oligonucleotide bond connectivity led to unique properties. UV melting temperature experiments indicate that the (2'-5')-oligo-3'-deoxyadenylates, (2'-5')-3'-dA8 and (2'-5')-3'-dA8(s) phosphorothioate, hybridize selectively to single-stranded RNA but not DNA. The complex (2'-5')-3'-dA8:poly (U) (Tm = 32 degrees C) was nearly as stable as the natural (3'-5')-2'-dA8 and poly (U) (Tm = 33 degrees C) in 130 mM NaCl, and 10 mM phosphate buffer (pH 7.5). However, no association was observed upon mixing (2'-5')-3'-dA8 and poly (dT). The (2'-5') linkages also confer greater resistance to exo- and endonucleolytic degradation compared with (3'-5')-linked oligomers. The rate of degradation of (2'-5')-3'-dA8 was almost four times less than that of (3'-5')-2'-dA8 in cell culture medium containing 10% heat-inactivated fetal calf serum. An increase in stability for (2'-5')-3'-dA8 against endonuclease activity was observed in both cytoplasmic and nuclear extracts. The nucleic acid selectivity of (2'-5')-oligo-3'-deoxynucleotides may represent an important design feature to improve the efficacy of antisense oligonucleotides.

Chemical nucleic acid synthesis, modification and labelling

The chemical synthesis of RNA on solid phase has now become routine using labile protecting groups and mild deprotection methods. The great interest in antisense technology has sparked the development of P-chiral phosphorothioates and a large number of DNA analogues with modified sugars and/or backbones to increase resistance to nucleases, and with modifier groups attached to the sugar, nucleobase or internucleotide function to aid cellular uptake.