A novel method for the synthesis of dinucleoside boranophosphates by a boranophosphotriester method

2'-Deoxyribonucleoside-3'-boranophosphates (nucleotide monomers), including four kinds of nucleobases, were synthesized in good yields by the use of new boranophosphorylating reagents. We have explored various kinds of condensing reagents as well as nucleophilic catalysts for the boranophosphorylation reaction with nucleosides. In the synthesis of dinucleoside boranophosphates, undesirable side reactions occurred at the O-4 of thymine and the O-6 of N2-phenylacetylguanine bases. To avoid these side reactions, additional protecting groups, benzoyl (Bz) and diphenylcarbamoyl (Dpc) groups, were introduced to thymine and guanine bases, respectively. As a result, the condensation reactions proceeded smoothly without any side reactions, and the dimers including four kinds of nucleobases were obtained in excellent yields. In the deprotection of the 5'-DMTr group, Et3SiH was found to be effective as a scavenger for the DMTr cation which caused a P-B bond cleavage. After removal of the other protecting groups by the conventional procedure, four kinds of dinucleoside boranophosphates were obtained in good yields.     

Efficient N-arylation and N-alkenylation of the five DNA/RNA nucleobases

A general approach to N-arylation and N-alkenylation of all five DNA/RNA nucleobases at the nitrogen atom normally attached to the sugar moiety in DNA or RNA has been developed. Various protected or masked nucleobases engaged readily in the copper-mediated Chan-Lam-Evans-modified Ullmann condensation with a range of different boronic acids at room temperature and were subsequently converted to the corresponding deprotected or unmasked adducts. Different N(3)-protecting groups were examined in the case of thymine, where the benzoyl group afforded the highest yields. A 4-alkylthio-substituted pyrimidin-2(1H)-one served as both a cytosine and a uracil precursor and was N-arylated and N-alkenylated in high yields. Adenine was efficiently and selectively N-arylated and N-alkenylated at the N(9) position by employing a bis-Boc-protected adenine derivative, while a bis-Boc-protected 2-amino-6-chloropurine served as guanine precursor and could also be selectively N(9)-arylated and N(9)-alkenylated.     

A Mild and Efficient Method for N‐Arylnucleobase Synthesis via the Cross‐Coupling Reactions of Nucleobases with Arylboronic Acids Catalyzed by Simple Copper Salts

A simple and efficient copper‐salt catalyzed N‐arylation of nucleobases is reported. In a mixed solvent of MeOH and H₂O, the coupling products were obtained in moderate to excellent yields at room temperature within a short time. A variety of substituted N‐aryl nucleobases can be prepared through this procedure.     

Solvent-free, microwave assisted 1,3-cycloaddition of nitrones with vinyl nucleobases for the synthesis of N,O-nucleosides

A number of 4′-aza-2′,3′-dideoxy nucleosides have been synthesized in good yields and short reaction times by straightforward microwave assisted 1,3-cycloaddition of vinyl nucleobases with nitrones, in the absence of solvent. The vinyl nucleobases are used, for the first time, in their unprotected form.     

A highly efficient protocol for the synthesis of N-aryl nucleobases using zinc oxide in ionic liquids

A highly efficient and simple method for the synthesis of N-aryl derivatives of pyrimidine and purine nucleobases via Narylation of nucleobases using zinc oxide in 1-butyl-3-methylimidazolium bromide ([bmim]Br) under microwave as well as thermal conditions is described. In both conditions, the title compounds were produced in high to excellent yields and in short reaction times.     

Tuning the gas phase redox properties of copper(II) ternary complexes of terpyridines to control the formation of nucleobase radical cations

Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) of ternary copper(II) complexes of [Cu(terpyX)(M)]2+ (where terpyX = is a substituted 2,2':6',2'-terpyridine ligand; M = the nucleobases: adenine, guanine, thymine and cytosine) was examined as a means of forming radical cations of nucleobases in the gas phase. The following substituents were examined: 4'-NMe2-2,2':6',6'-terpyridine; 4'-OH-2,2':6',6'-terpyridine; 4'-F-2,2':6',6'-terpyridine; 2,2':6',6'-terpyridine; 4'-Cl-2,2':6',6'-terpyridine; 4'-Br-2,2':6',6'-terpyridine; 4'-CO2H-2,2':6',6'-terpyridine; 4'-NO2-2,2':6',6'-terpyridine and 6,6'-dibromo-2',2:6',2'-terpyridine. Each of the ternary complexes [Cu(terpyX)(M)]2+ was mass selected and subjected to collision induced dissociation (CID) in a quadrupole ion trap. The types of fragmentation reactions observed for these complexes depend on the nature of the substituent on the terpyridine ligand, while the yields of the radical cations of the nucleobases follow the order of their ionization energies (IEs): G (lowest IE) > A > C > T (highest IE). In general, radical cation formation is favoured for electron withdrawing substituents (e.g. NO2) while loss of the neutral nucleobase is favoured for electron donating substituents (e.g. NMe2). Loss of the protonated nucleobase is a major fragmentation pathway for the OH substituted terpyridine system, consistent with its ability to bind to a metal centre as a deprotonated ligand. Crystal structure determinations of (6,6'-dibromo-2',2:6',2'-terpyridine)bis(nitrato)copper(II) and diaqua(4'-oxo-2,2':6',6'-terpyridine)copper(II) nitrate monohydrate were performed and correlated with the ESI results.     

Preparation of supramolecular chromophoric assemblies using a DNA duplex

Organization of supramolecular assemblies of chromophores with precisely-controlled orientation and sequence remains challenging. Nucleic acids with complementary base sequences spontaneously form double-helical structures. Therefore, covalent attachment of chromophores to DNA or RNA can be used to control assembly and orientation of chromophores. In this perspective, we first review our recent work on the assemblies of fluorophores (pyrene and perylene) by using natural base pairs. The interaction between dyes can be strictly controlled by means of cluster and interstrand wedge motifs. We then discuss novel artificial base pairs that can suppress the interaction between fluorophores and nucleobases. We incorporated a cyclohexane moiety into DNA, and showed that these artificial base pairs suppressed the electron-hole transfer between fluorophores and nucleobases and enhanced the quantum yields of fluorophores. These base pairs can potentially be used to accumulate fluorophores inside DNA duplexes without decreasing quantum yields.     

A computational and experimental study of cation affinity (Na+) of nucleobases and modified nucleobases by electrospray ionization ion trap mass spectrometry

Gas-phase Na+ affinities of modified or unmodified nucleobases were determined theoretically at the density functional theory level, with the B3P86 functional and the 6-31 + G* basis set, and experimentally using electrospray ionization ion trap mass spectrometry (ESI-ITMS) and the kinetic method. For the calculations, the sodium cation affinities (SCA) were obtained from energies of the most stable complexes of the free nucleobases. Experimentally and theoretically relative scales of cation affinities were determined using eight modified and unmodified nucleobases and a very good agreement was obtained.     

One-pot synthesis of N-alkyl purine and pyrimidine derivatives from alcohols using TsIm: a rapid entry into carboacyclic nucleoside synthesis

A convenient and efficient one-pot N-alkylation of nucleobases from alcohols using N-(p-toluenesulfonyl)imidazole (TsIm) is described. In this method, treatment of alcohols with a mixture of purine or pyrimidine nucleobase, TsIm, K₂CO₃, and triethylamine in refluxing DMF regioselectively furnishes the corresponding N-alkyl nucleobases in good yields. This methodology is highly efficient for various structurally diverse primary alcohols.     

Microwave-promoted facile and efficient preparation of N-(alkoxycarbonylmethyl) nucleobases--building blocks for peptide nucleic acids

A simple, rapid, and regioselective approach for the synthesis of N-(methoxy-carbonylmethyl)- and N-(n-propoxycarbonylmethyl) nucleobases was developed. By using DMF as the solvent and in the presence of K2CO3 as the base, all the desired products were obtained in moderate yields within 8 min under microwave irradiation.     

Synthesis of Acyclic Nucleosides with N‐[(Benzyloxy)(aryl)methyl] Substituents as Potential HEPT,EBPU, and TNK‐651 Analogues

The syntheses of the novel acyclic nucleosides 5a – 5m , carrying different N‐[(benzyloxy)(aryl)methyl] substituents, are described (Scheme). These compounds could be prepared in medium‐to‐good yields by either direct or silyl‐assisted coupling of the electrophiles 6 with either purine or pyrimidine nucleobases, or with different imidazole derivatives. The reactivity of the positively charged electrophilic intermediates derived from 6 upon Cl^? abstraction was rationalized by ab initio HF/6‐311G quantum‐mechanic calculations. The positive charge was found to be dispersed differently, depending on the electronic properties of the aryl substituents.     

Synthesis of racemic and enantiomeric 3-pyrrolidinyl derivatives of nucleobases

The synthesis of novel 3-pyrrolidinyl derivatives of nucleobases is described. Starting from malic acid, we improved the synthesis of both racemic and optically active N-benzyl-3-hydroxypyrrolidine-2,5-diones, which were transformed in four steps into N-tert-butyloxycarbonyl-3-mesyloxypyrrolidines, the key synthons for the alkylation of purine and pyrimidine nucleobases. Alkylations of cesium salts of purines and sodium salts of pyrimidines with N-tert-butyloxycarbonyl-3-mesyloxypyrrolidines proceeded smoothly, giving high yields of 9-substituted purine derivatives and moderate yields of 1-substituted pyrimidine derivatives. Using (S)-N-tert-butyloxycarbonyl-3-mesyloxypyrrolidine as the same intermediate for the synthesis of both enantiomeric N-Boc-3-pyrrolidinyladenines, and considering the results obtained on chiral HPLC analysis of the products, we proved that nucleophilic displacement of the mesyloxy group proceeded with inversion and not with retention of the configuration. Prepared compounds were tested for cytostatic and antiviral properties, but no significant activity was found.     

Solid-phase synthesis of oligodeoxyribonucleoside boranophosphates by the boranophosphotriester method

Oligodeoxyribonucleoside boranophosphates (BH3-ODNs), containing four kinds of nucleobases, were synthesized by the solid-phase boranophosphotriester method. The 2'-deoxyribonucleoside 3'-boranophosphate monomers having 2-cyanoethyl (CE) groups as the phosphorus protecting groups were synthesized in good yields. A new condensing reagent, 1,3-dimethyl-2-(3-nitro-1,2,4-triazol-1-yl)-2-pyrrolidin-1-yl-1,3,2-diazaphospholidinium hexafluorophosphate, was found to be highly effective for the condensation reaction on the solid support. We also found that 1,8-bis(N,N-dimethylamino)naphthalene could accelerate the condensation reaction without causing beta-elimination of the CE groups from the boranophosphate triesters. The internucleotidic CE groups were selectively removed by treatment with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) under anhydrous conditions. The acetylation of the terminal 5'-hydroxy group was found to be effective to suppress the decomposition of the BH3-ODNs during the DBU treatment on the solid support. Under optimized conditions for the solid-phase synthesis and the deprotection reactions, BH3-ODNs (4mers and 12mers) containing four kinds of nucleobases were synthesized in good yields. The hybridization properties of the BH3-ODN 12mers with the complementary native DNAs and RNAs were determined by the thermal denaturing studies. In contrast to the low thermal melting (Tm) value of the duplex composed of T((PB)T)11 and native dA12 (12.8 degrees C), the duplex consisting of d(C(PB)A(PB)G(PB)T)3 and d(ACTG)3 showed a higher Tm value (44.7 degrees C) under high-salt conditions. Furthermore, d(C(PB)A(PB)G(PB)T)3 formed a more stable duplex with the complementary RNA, r(ACUG)3 with a Tm value of 50.5 degrees C. Thus, we first demonstrated that the binding affinity of BH3-ODN to a complementary DNA or RNA is dramatically increased, owing to the inclusion of the four kinds of nucleobases.     

Click to fit: versatile polyvalent display on a peptidomimetic scaffold

We describe an efficient protocol to effect multisite conjugation reactions to oligomers on solid-phase support. Sequence-specific N-substituted glycine "oligopeptoids" were utilized as substrates for azide-alkyne cycloaddition reactions. Diverse groups, including nucleobases and fluorophores, were conjugated at up to six positions on peptoid side chains with yields ranging from 88 to 96%. This strategy will be broadly applicable for generating polyvalent displays on peptides and other scaffolds, allowing precise control of spacing between the displayed groups.     

Triphenylphosphine-free approach for one-pot N-alkylation of purine,pyrimidine, and azole derivatives with alcohols using P2O5/KI: A facile and selective route to access carboacyclic nucleosides

A facile, selective, and mild synthetic approach for one-pot N-alkylation of nucleobases and other related N-heterocycles via alcohols, using a mixture of P₂O₅ and KI is described. The reaction of structurally diverse purines, pyrimidines, and/or azoles with primary alcohols with the use of P₂O₅/KI and basic mixture of Et₃N/K₂CO₃ in refluxing DMF affords the corresponding N-alkyl derivatives (carboacyclic nucleosides) in good to reasonable yields. The influence of different parameters comprising solvent, base, temperature, and substrate/reagent ratios was assessed on the reaction progress. The secondary and tertiary alcohols were failed to react with nucleobases. The main advantageous of current protocol is formation of water soluble side products in which provides simple work-up and purification processes.     

Calix[6]arene acetic acid extraction behavior and specificity with respect to nucleobases

The extraction behavior of various nucleobases was investigated with a series of calixarene derivatives. A calix[6]arene acetic acid was found to extract around 80% of adenine from an aqueous phase, and showed the highest specificity for adenine among all the nucleobases tested. The important factors influencing the recognition properties of calixarene were discovered to be its cyclic structure, its cavity size, and the functional carboxylic acid groups. The carbonyl group and the position of the amino group in the guest molecules also affect the extraction efficiency. Calix[6]arene forms a stable 1:1 complex with adenine by entrapping it into the cavity. Adenine was readily recovered from the organic phase by contacting with a fresh acidic solution.     

Molecular-recognition properties of a water-soluble cucurbit[6]uril analogue

The molecular-recognition properties of the cucurbit[6]uril analogue (1) in aqueous buffer (sodium acetate, 50 mM, pH 4.74, 25 degrees C) toward a variety of guests including alkanediamines (6-12), aromatics (14-32), amino acids (33-36), and nucleobases (37-42) were studied by fluorescence spectroscopy. For the alkanediamines studied (H2N(CH)nNH2, n = 6, 7, 8, 9, 10, 11, 12), the association constants increase as the length of the alkane (n) is increased. Host 1 is capable of forming strong complexes with guests containing aromatic rings with association constants (Ka) ranging from 10(2) to 10(6) M(-1) as a result of the favorable pi-pi interactions that occur between host 1 and the aromatic rings of the guest when bound in the cavity of 1. Biologically relevant guests such as amino acids and nucleobases are also bound in the cavity of 1 with Ka values ranging from 10(3) to 10(6) M(-1). Consequently, cucurbit[6]uril analogue 1 functions as a versatile fluorescent sensor for the presence of a wide range of chemically and biologically important substances in aqueous solution including nitroaromatics, neurotransmitters, amino acids, and nucleobases.     

Unimolecular depurination of protonated deoxyribonucleosides in the gas phase: A fast atom bombardment tandem mass spectrometric investigation

The spontaneous or collision-induced unimolecular dissociations of base-protonated 2′-deoxyribonucleosides afford, in the gas phase and in the absence of solvent, high yields of protonated nucleobases. The release of neutral bases corresponds to a high-energy reaction path and does not compete with the formation of the protonated bases. A determinant solvent effect has to be invoked to explain the opposite behaviour, which is exhibited by the same precursors, dissociating unimolecularly, in aqueous acidic solution.     

Direct Chemoselective Synthesis of N-3-Substituted Pyrimidinones in a Microwave-Assisted Method

Synthesis of selectively N-3-substituted pyrimidine nucleobases or pyrimidinones has always been a challenge because of poor regioselectivity and chemoselectivity. In this article we demonstrate a single-step, de novo synthesis of selectively N-3-substituted modified pyrimidinones. We have developed a microwave-assisted methodology for direct, chemoselective alkylation, benzylation, and arylation of C-5 and C-6 substituted pyrimidine nucleobases selectively at the N-3 position. The reactions were found to proceed, with high efficiency, without the requirement of solvent and were complete within 10–15 min of irradiation. The efficiency of the method was further improved by addition of a Lewis acid, which not only increases the yield significantly but also accelerates the reaction rate.     

Effect of Alkali Metal Cations on Length and Strength of Hydrogen Bonds in DNA Base Pairs

For many years, non-covalently bonded complexes of nucleobases have attracted considerable interest. However, there is a lack of information about the nature of hydrogen bonding between nucleobases when the bonding is affected by metal coordination to one of the nucleobases, and how the individual hydrogen bonds and aromaticity of nucleobases respond to the presence of the metal cation. Here we report a DFT computational study of nucleobase pairs interacting with alkali metal cations. The metal cations contribute to the stabilization of the base pairs to varying degrees depending on their position. The energy decomposition analysis revealed that the nature of bonding between nucleobases does not change much upon metal coordination. The effect of the cations on individual hydrogen bonds were described by changes in VDD charges on frontier atoms, H-bond length, bond energy from NBO analysis, and the delocalization index from QTAIM calculations. The aromaticity changes were determined by a HOMA index.