A linchpin carbacyclization approach for the synthesis of carbanucleosides

A convenient synthesis of carbanucleosides, with both enantiomers equally accessible, is reported. The key step is a tandem linchpin cyclization process to give access to substituted carbafuranose derivatives having the correct relative stereochemistry for subsequent nucleobase introduction with inversion of configuration at C1. This was illustrated by the synthesis of 2',3'-dideoxycarbathymidine via a convergent nucleobase introduction and of 2',3'-dideoxy-6'-hydroxycarbauridine via a linear nucleobase introduction. Both methods relied on Mitsunobu chemistry, and the first example of the Mukaiyama modification of the Mitsunobu reaction involving nucleobases as nucleophiles is reported.     

Convenient synthesis of nucleoside and isonucleoside analogues

[reaction: see text]. A very simple methodology to stereoselectively achieve tricyclic isonucleosides (nucleobase = thymine, uracil, and 5-fluoruracil) and 3'-C-branched nucleosides (nucleobase = theophylline) was performed by means of a DBU-mediated addition process using a readily available 2-bromo sugar. The mechanism for these transformations implies the loss of both substituents at C-2 and C-3 on the sugar moiety, and although it seems that DBU is probably involved, its involvement has not yet been ascertained. Cytosine did not react under these conditions.     

A new class of phosphanucleosides containing a 3-hydroxy-1-hydroxymethylphospholane 1-oxide ring

Novel phosphanucleosides containing a 3-hydroxy-1-hydroxymethylphospholane 1-oxide ring were synthesized as compounds with potential biological activity. A double Arbuzov reaction was employed to prepare a phospholene precursor, which was then converted into an epoxide and subsequently into racemic phosphanucleoside via nucleobase construction.     

A new entry to carbocyclic nucleosides: oxidative coupling reaction of cycloalkenylsilanes with a nucleobase mediated by hypervalent iodine reagent

A novel method for synthesizing carbocyclic nucleosides was developed. The new synthesis includes a direct coupling reaction of cycloalkenylsilanes with a silylated nucleobase catalyzed by a hypervalent iodine reagent. By applying the method, a novel carbocyclic cytidine derivative having bis(hydroxymethyl)cyclohexene as a pseudosugar moiety, designed as a potential anti-HIV agent, was successfully synthesized.     

A kinetic and thermodynamic study of the glycosidic bond cleavage in deoxyuridine

Density functional theory was used to study the thermodynamics and kinetics for the glycosidic bond cleavage in deoxyuridine. Two reaction pathways were characterized for the unimolecular decomposition in vacuo. However, these processes are associated with large reaction barriers and highly endothermic reaction energies, which is in agreement with experiments that suggest a (water) nucleophile is required for the nonenzymatic glycosidic bond cleavage. Two (S(N)1 and S(N)2) reaction pathways were characterized for direct hydrolysis of the glycosidic bond by a single water molecule; however, both pathways also involve very large barriers. Activation of the water nucleophile via partial proton abstraction steadily decreases the barrier and leads to a more exothermic reaction energy as the proton affinity of the molecule interacting with water increases. Indeed, our data suggests that the barrier heights and reaction energies range from that for hydrolysis by water to that for hydrolysis by the hydroxyl anion, which represents the extreme of (full) water activation (deprotonation). Hydrogen bonds between small molecules (hydrogen fluoride, water, or ammonia) and the nucleobase were found to further decrease the barrier and overall reaction energy but not to the extent that the same hydrogen-bonding interactions increase the acidity of the nucleobase. Our results suggest that the nature of the nucleophile plays a more important role in reducing the barrier to glycosidic bond cleavage than the nature of the small molecule bound, and models with more than one hydrogen fluoride molecule interacting with the nucleobase provide further support for this conclusion. Our results lead to a greater fundamental understanding of the effects of the nucleophile, activation of the nucleophile, and interactions with the nucleobase for this important biological reaction.     

Synthesis and characterization of nucleobase functionalized monothiophenes

The synthesis of a series of nucleobase functionalized thiophene monomers has been accomplished through the reaction of 2-bromo-1-thiophen-3-yl-ethanone with the corresponding DNA base anion. The distinctive pK_a values for the various amine groups in the nucleobases provided a pathway for the creation of specific anions through selective deprotonation of these groups. Using the appropriate anion it is possible to create an amine linkage between the thiophene and nucleobase that is, analogous to that found between the deoxyribose sugar and nucleobase, in the biologically occurring nucleoside.     

Selective one-electron oxidation of duplex DNA oligomers: reaction at thymines

The one-electron oxidation of duplex DNA generates a nucleobase radical cation (electron "hole") that migrates long distances by a hopping mechanism. The radical cation reacts irreversibly with H2O or O2 to form oxidation products (damaged bases). In normal DNA (containing the four common DNA bases), reaction occurs most frequently at guanine. However, in DNA duplexes that do not contain guanine (i.e., those comprised exclusively of A/T base pairs), we discovered that reaction occurs primarily at thymine and gives products resulting from oxidation of the T-C5 methyl group and from addition to its C5-C6 double bond. This surprising result shows that it is the relative reactivity, not the stability, of a nucleobase radical cation that determines the nature of the products formed from oxidation of DNA. A mechanism for reaction is proposed whereby a thymine radical cation may either lose a proton from its methyl group or H2O/O2 may add across its double bond. In the latter case, addition may initiate a tandem reaction that converts both thymines of a TT step to oxidation products.     

A 4-[(3R,4R)-dihydroxypyrrolidino]pyrimidin-2-one nucleobase for a CG base pair in triplex DNA

In order to expand target sequences in triplex DNA formation, the development of a nucleobase that recognizes a CG base pair in dsDNA was attempted. A 4-[(3R,4R)-dihydroxypyrrolidino]pyrimidin-2-one nucleobase was found to recognize a CG base pair with high sequence-selectivity.     

Synthesis of oligodeoxynucleotides using fully protected deoxynucleoside 3'-phosphoramidite building blocks and base recognition of oligodeoxynucleotides incorporating N3-cyano-ethylthymine

Oligodeoxynucleotide (ODN) synthesis, which avoids the formation of side products, is of great importance to biochemistry-based technology development. One side reaction of ODN synthesis is the cyanoethylation of the nucleobases. We suppressed this reaction by synthesizing ODNs using fully protected deoxynucleoside 3'-phosphoramidite building blocks, where the remaining reactive nucleobase residues were completely protected with acyl-, diacyl-, and acyl-oxyethylene-type groups. The detailed analysis of cyanoethylation at the nucleobase site showed that N3-protection of the thymine base efficiently suppressed the Michael addition of acrylonitrile. An ODN incorporating N3-cyanoethylthymine was synthesized using the phosphoramidite method, and primer extension reactions involving this ODN template were examined. As a result, the modified thymine produced has been proven to serve as a chain terminator.     

Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis

The hairpin ribozyme catalyzes a reversible phosphodiester cleavage reaction. We examined the roles of conserved nucleobases in catalysis using an abasic ribozyme rescue strategy. Loss of the active site G8 nucleobase reduced the cleavage rate constant by 350-fold while loss of A9 and A10 nucleobases reduced activity less than 10-fold. Certain heterocyclic amines restored partial activity when provided in solution to the variant lacking G8. Heterocyclic amines that were capable of rescue shared the exocyclic amine and cyclic amide in common with the Watson-Crick hydrogen bonding face of guanine. In contrast to the shallow pH dependence of unmodified ribozyme activity, rescue activity increased sharply with decreasing pH. These results support a novel model for RNA catalysis in which a cationic nucleobase contributes electrostatic stabilization to negative charge developing in the transition state.     

Ferrocene-linked thymine/uracil conjugates: base pairing directed self-assembly and supramolecular packing

Ferrocene-linked bis(nucleobase) (1a-c) and chimeric nucleobase (1d) conjugates have been synthesized from mono- and bis(hydroxybutyl)ferrocene 6 via Mitsunobu reaction as the key step. X-ray crystallographic studies of ferrocene bis(nucleobase) conjugates reveal two-dimensional supramolecular organizations of backbones through self-assembled Watson-Crick and reverse Watson-Crick type pairs. Ferrocene-bis(thymine) conjugate self-assembles by reverse Watson-Crick pairing, while the corresponding bis(uracil) conjugate self-assembles by alternating WC and reverse WC type pairing. Such continuous assemblies are not seen in monosubstituted ferrocene nucleobase conjugates which form only planar sheets. The results are interesting from the point of understanding and engineering supramolecular assemblies through rational design of base pairing patterns.     

Clickable Nucleic Acids: Sequence‐Controlled Periodic Copolymer/Oligomer Synthesis by Orthogonal Thiol‐X Reactions

Synthetic polymer approaches generally lack the ability to control the primary sequence, with sequence control referred to as the holy grail. Two click chemistry reactions were now combined to form nucleobase‐containing sequence‐controlled polymers in simple polymerization reactions. Two distinct approaches are used to form these click nucleic acid (CNA) polymers. These approaches employ thiol–ene and thiol‐Michael reactions to form homopolymers of a single nucleobase (e.g., poly(A)_n) or homopolymers of specific repeating nucleobase sequences (e.g., poly(ATC)_n). Furthermore, the incorporation of monofunctional thiol‐terminated polymers into the polymerization system enables the preparation of multiblock copolymers in a single reaction vessel; the length of the diblock copolymer can be tuned by the stoichiometric ratio and/or the monomer functionality. These polymers are also used for organogel formation where complementary CNA‐based polymers form reversible crosslinks.     

Facile deprotection of O-Cbz-protected nucleosides by hydrogenolysis: an alternative to O-benzyl ether-protected nucleosides

[reaction: see text] Because of side-reactions encountered during hydrogenolysis, benzyl ethers are usually not an effective protecting group for nucleosides. Benzyloxycarbamates provide an alternative to traditional benzyl ethers for protection of nucleoside hydroxyl groups, as they are much more labile to hydrogenolysis. Deprotection conditions using transfer hydrogenolysis are described that avoid the reduction of the pyrimidine nucleobase during deblocking of O-Cbz-protected nucleosides. Additionally, an experiment is described that suggests the nucleobase component of a nucleoside is responsible for the sluggish hydrogenolysis of nucleosides.     

Mechanism and control of rare tautomer trapping at a metal-metal bond: adenine binding to dirhodium antitumor agents

The cause of mutations in the genome by the occurrence of nuclebases in their rare tautomeric forms was first proposed by Watson and Crick in 1953. Since this pioneering proposal, tremendous experimental and theoretical research efforts have aimed to elucidate the conditions under which nucleobase tautomerizations can occur. Previous work raised the interesting question as to whether adenine binding to the anticancer drug cisplatin can induce tautomerization of the nucleobase, but the results indicated such an event to be unlikely under physiological conditions. In this work, we have studied the reaction of three adenine (Ade) tautomers with metal-metal bonded dirhodium antitumor agents using high-level computations. The calculations reveal that the thermodynamically most stable compound in the reaction of Ade with dirhodium tetraformate in aqueous solution is a species in which a rare N6-imino tautomer spans the metal-metal bond via sites N7 and N6. However, comprehensive transition state predictions suggest that the multiple-step mechanisms leading to this bridging species are kinetically highly challenging. A number of strategies to chemically modify the metal-metal unit are considered, aiming to derive a rational plan for trapping the rare N6-imino tautomer, which is incapable of Watson-Crick pairing with canonical thymine.     

New synthesis of (+/-)-isonucleosides

[Structure: see text] A novel method for synthesizing isonucleosides, a new class of anti-HIV nucleosides, is described. 2,2-Dimethyl-1,3-dioxan-5-one was converted into a dioxabicyclohexane derivative in six steps. After cleaving the epoxide group with thiophenol, the resulting product was subjected to the Mitsunobu reaction in the presence of a nucleobase to give the desired isonucleoside derivative via migration of the thiophenyl group. Removal of the thiophenyl group under radical conditions followed by deprotection led to the 4'-substituted 2',3'-dideoxyisonucleosides as a racemic mixture.     

Synthesis,incorporation into triplex-forming oligonucleotide,and binding properties of a novel 2'-deoxy-C-nucleoside featuring a 6-(thiazolyl-5)benzimidazole nucleobase

[reaction: see text] 6-(Thiazolyl-5)benzimidazole (B(t)()) was designed as a novel nucleobase for the specific recognition of an inverted A.T base pair in a triple helix motif. It was successfully incorporated into an 18-mer triplex-forming oligonucleotide (TFO) using the 2'-deoxy-C-nucleoside phosphoramidite 16. The triple helix binding properties of the modified TFO were examined by means of thermal denaturation experiments targeting an oligopyrimidine.oligopurine 26-mer DNA duplex containing an A.T base pair inversion.     

DNA-binding small-ligand-immobilized surface plasmon resonance biosensor for detecting thymine-related single-nucleotide polymorphisms

A surface plasmon resonance (SPR) biosensor that carries DNA-binding small ligands has been developed for the detection of single-nucleotide polymorphisms (SNPs). 3,5-Diaminopyrazine derivatives, with a hydrogen-bonding profile fully complementary to the thymine base, were utilized as recognition elements on the sensor surface, and a target single-stranded DNA sequence was hybridized with a DNA probe containing an abasic site to place this site opposite a nucleobase to be detected. In a continuous flow of sample solutions buffered to pH 6.4 (0.25 M NaCl), the 3,5-diaminopyrazine-based SPR sensor can detect an orphan nucleobase in the duplex with a clear selectivity for thymine over cytosine, guanine, and adenine (5'-GTT GGA GCT GXG GGC GTA GGC-3'/3'-CAA CCT CGA CNC CCG CAT CCG-5'; X=abasic site, N=target nucleobase G, C, A, or T). The SPR response was linear in the concentration range 10-100 nM. Allele discrimination is possible based on the combination of different binding surfaces in a flow cell of the SPR system, which is demonstrated for the analysis of the thymine/cytosine mutation present in 63-meric polymerase chain reaction (PCR) amplification products (Ha-ras gene, codon 12, antisense strand). Comparison with a bulk assay based on 3,5-diaminopyrazine/DNA binding shows that the immobilization of 3,5-diaminopyrazine derivatives on the SPR sensor allows more sensitive detection of the target DNA sequence, and binding selectivity can be tuned by controlling the salt concentration of sample solutions. These features of the DNA-binding small-molecule-immobilized SPR sensor are discussed as a basis for the design of SPR biosensors for SNP genotyping.     

Nitromethane as a scavenger of acrylonitrile in the deprotection of synthetic oligonucleotides

A novel deprotection procedure for synthetic oligonucleotides was developed to prevent nucleobase alkylation. Acrylonitrile, a side product of the deprotection of a 2-cyanoethyl phosphate protecting group and which causes nucleobase alkylation, was found to be trapped by the addition of some acidic compounds, which generate a carbanion species under the conventional deprotection conditions using aqueous NH₃. The 2-cyanoethylation of thymidine was inhibited effectively in the presence of nitromethane.     

Enantioselective syntheses of carbanucleosides from the Pauson-Khand adduct of trimethylsilylacetylene and norbornadiene

A new enantioselective approach to carbanucleosides from Pauson-Khand (PK) adduct 1 is disclosed. The chiral cyclopentenone 1 is readily accessible in enantiomerically pure form via PK reaction of trimethylsilylacetylene and norbornadiene using N-benzyl-N-diphenylphosphino-tert-butyl-sulfinamide as a chiral P,S ligand. (-)-Carbavir and (-)-Abacavir were enantioselectively synthesized starting from (-)-1. The key steps of the sequence are a photochemical conjugate addition of a hydroxymethyl radical, a retro-Diels-Alder reaction, and a palladium catalyzed allylic substitution to introduce the nucleobase.     

2,6-Diamino-5,8-diaza-7,9-dicarba-purine

[reaction: see text] The title compound, a constitutional isomer of the natural nucleobase 2,6-diaminopurine, undergoes regioselective electrophilic substitutions at carbon C-9.