The chemical synthesis of the anticodon loop of an eukaryotic initiator tRNA containing the hypermodified nucleoside N6-/N-threonylcarbonyl/-adenosine/t6A/1

Efficient access to 3'-O-phosphoramidite derivatives of tRNA related N 6-threonylcarbamoyladenosine (t6A) and 2-methylthio-N 6-threonylcarbamoyladenosine (ms2t6A)

An efficient method of ureido linkage formation during epimerization-free one-pot synthesis of protected hypermodified N 6-threonylcarbamoyladenosine (t6A) and its 2-SMe analog (ms2t6A) was developed. The method is based on a Tf2O-mediated direct conversion of the N-Boc-protecting group of N-Boc-threonine into the isocyanate derivative, followed by reaction with the N 6 exo-amine function of the sugar protected nucleoside (yield 86-94%). Starting from 2',3',5'-tri-O-acetyl protected adenosine or 2-methylthioadenosine, the corresponding 3'-O-phosphoramidite monomers were obtained in 48% and 42% overall yield (5 step synthesis). In an analogous synthesis, using the 2'-O-(tert-butyldimethylsilyl)-3',5'-O-(di-tert-butylsilylene) protection system at the adenosine ribose moiety, the t6A-phosphoramidite monomer was obtained in a less laborious manner and in a remarkably better yield of 74%.

A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification

N(6)-threonylcarbamoyladenosine (t(6)A) is a universally conserved, essential modified nucleoside found in transfer RNAs (tRNAs) responsible for ANN codons in all three domains of life. t(6)A has a crucial role in maintaining decoding accuracy during protein synthesis. The presence of t(6)A in cellular tRNAs has been well documented for more than four decades. However, under conditions optimized for nucleoside preparation, we detected little t(6)A in tRNAs from Escherichia coli. Instead, we identified a new modified base named 'cyclic t(6)A' (ct(6)A), which is a cyclized active ester with an oxazolone ring. An E1-like enzyme, CsdL (renamed as TcdA), which catalyzes ATP-dependent dehydration of t(6)A to form ct(6)A, was also identified. Two yeast homologs of tcdA, YHR003C (TCD1) and YKL027W (TCD2), were required for ct(6)A formation and respiratory cell growth. ct(6)A was involved in promoting decoding efficiency. Structural modeling suggests that ct(6)A recognizes the first adenine base of ANN codon at the ribosomal A site.

Impact of histidine residue on chelating ability of 2'-deoxyriboadenosine

Copper(II) complexes with a new chelator-type nucleoside-histidine modified 2'-deoxyriboadenosine (N-[(9-β-D-2'-deoxyribofuranosylpurin-6-yl)-carbamoyl]histidine) were studied by potentiometric and spectroscopic (UV-visible, CD, EPR) techniques, in conjunction with computer modeling optimization. The ligand can act as bidentate or tridentate depending on pH range. In acidic pH a very stable dimeric complex Cu(2)L(2) predominates with coordination spheres of both metal ions composed of oxygen atoms from carboxylic groups, one oxygen atom from ureido group and two nitrogen atoms derived from purine base and histidine ring. Above pH 5, deprotonation of carbamoyl nitrogens leads to the formation of CuL(2), Cu(2)L(2)H(-1) and Cu(2)L(2)H(-2) species. The CuL(2)H(-1) and CuL(2)H(-2) complexes with three or four nitrogens in Cu(II) coordination sphere have been detected in alkaline medium. Our findings suggest that N-[(9-beta-D-2'-deoxyribofuranosylpurin-6-yl)-carbamoyl]histidine chelates copper(II) ions very efficiently. The resulting complex might be used as an alternative base-pairing mode in which hydrogen-bonded base pairs present in natural DNA are replaced by metal-mediated ones.

Synthesis of oligoribonucleotides containing N6-alkyladenosine and 2-methylthio-N6-alkyladenosine

The N(6)-alkyladenosines and 2-methylthio-N(6)-alkyladenosines are the most common modified adenosine nucleosides, and transfer ribonucleic acids (tRNA) are particularly rich in these modified nucleosides. They are present at position 37 of the anticodon arm, and the contributions of these hypermodified nucleosides to codon-anticodon interactions as well as to translation are significant, although they are not fully understood. This unit describes a new chemical synthesis method for oligoribonucleotides containing N(6)-alkyladenosines and 2-methylthio-N(6)-alkyladenosines via postsynthetic modifications of precursor oligoribonucleotides. To obtain oligoribonucleotides containing N(6)-alkyladenosines, a precursor oligoribonucleotide carrying 6-methylthiopurine riboside residues was used, whereas for the synthesis of oligoribonucleotides containing 2-methylthio-N(6)-alkyladenosines, a precursor oligoribonucleotide carrying the 2-methylthio-6-chloropurine riboside was applied. This allowed synthesis of modified oligoribonucleotides containing naturally occurring modified nucleosides such as N(6)-isopentenyladenosine (i(6)A), N(6)-methyladenosine (m(6)A), 2-methylthio-N(6)-isopentenyladenosine (ms(2)i(6)A), and 2-methylthio-N(6)-methyladenosine (ms(2)m(6)A), as well as several unnaturally modified adenosine derivatives.

Convenient synthesis of N-unprotected deoxynucleoside 3'-phosphoramidite building blocks by selective deacylation of N-acylated species and their facile conversion to other N-functionalized derivatives

[reaction: see text] A new route to N-unprotected deoxynucleoside 3'-phosphoramidite building blocks by use of highly selective N-deacylation of commercially available N-acylated deoxynucleoside 3'-phosphoramidites is described. These compounds could be readily converted to other types of N-protected species by facile N-acylations with acylating reagents.

O-selectivity and utility of phosphorylation mediated by phosphite triester intermediates in the N-unprotected phosphoramidite method

Previously, O-selective phosphorylation on polymer supports in the N-unprotected phosphoramidite method could not be carried out because the amino groups of dA and dC have high reactivity toward tervalent phosphorus(III)-type phosphitylating reagents. In this paper, we developed a new coupling strategy named the "activated phosphite method" in which the phosphitylation is mediated by phosphite triester intermediates 1. Application of 1-hydroxybenzotriazole as the promoter to the solid-phase synthesis resulted in excellent O-selectivity of more than 99.7%. This O-selectivity was explained by the frontier molecular orbital interactions between the reactive intermediates and the nucleophiles such as the amino or hydroxyl groups of nucleosides. Furthermore, longer oligonucleotides were synthesized not only by a manual operation but also by a DNA synthesizer. The utility of our new method was demonstrated by the successful synthesis of a base-labile modified oligodeoxyribonucleotide having 4-N-acetyldeoxycytidine residues. Finally, DNA 20-mers containing dA or dC could be synthesized in good yields by use of a combined reagent of 6-trifluoromethyl-1-hydroxybenzotriazole and benzimidazolium triflate.

DNA synthesis without base protection

DNA synthesis can be achieved by using O-selective methods for internucleotide bond formation. This greatly simplifies the synthesis of oligodeoxyribonucleotides by eliminating the need for nucleobase protection and deprotection steps. This unit describes strategies that can be used for DNA synthesis without base protection. The discussion includes synthesis of phosphoramidite and H-phosphonate monomers, solid-phase assembly by the phosphoramidite and H-phosphonate methods, and future prospects for DNA synthesis using N-unprotected approaches.

The synthesis of oligoribonucleotides containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines via post-synthetic modification of precursor oligomers

The N6-alkyladenosines and 2-methylthio-N6-alkyladenosines are the most common modified adenosine nucleosides and transfer ribonucleic acids (tRNA) are particularly rich in these modified nucleosides. They are present at position 37 of the anticodon arm and the contribution of these hypermodified nucleosides to codon-anticodon interactions, as well as translation, are significant, although not fully understood. Herein we described a new chemical synthesis method of the oligoribonucleotides containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines via post-synthetic modifications of precursor oligoribonucleotides. To obtain oligoribonucleotides containing N6-alkyladenosines, the precursor oligoribonucleotide carrying 6-methylthiopurine riboside residue was used, whereas for the synthesis of oligoribonucleotides containing 2-methylthio-N6-alkyladenosines the precursor oligoribonucleotide carrying the 2-methylthio-6-chloropurine riboside was applied. Among the modified oligoribonucleotides of different length and secondary structures, there were several containing naturally occurring modified nucleosides such as: N6-isopentenyladenosine (i6A), N6-methyladenosine (m6A), 2-methylthio-N6-isopentenyladenosine (ms2i6A), and 2-methylthio-N6-methyladenosine (ms2m6A), as well as several unnaturally modified adenosine derivatives.

Proton-block strategy for the synthesis of oligodeoxynucleotides without base protection, capping reaction, and P-N bond cleavage reaction

A new N-unprotected phosphoramidite method called the "proton-block" approach was developed for the chemical synthesis of oligodeoxynucleotides based on the hitherto simplest and rational principle of acid-base reactions. This concept involves protection of the nucleobases of deoxycytidine and deoxyadenosine with "protons" to convert them to unreactive protonated bases during condensation by use of promoters having pK(a) values lower than 2.8. This strategy was applied to the synthesis of d[CpT] and d[ApT] to check the side reactions associated with the base residues. In this "proton-block" method, 5-nitrobenzimidazolium triflate (NBT) was found to be the best promoter, and THF was superior to CH(3)CN as the solvent so that the concomitant detritylation due to the inherent acidity of the promoter could be greatly suppressed. Application of this strategy to the solid-phase synthesis gave d[CpT], d[ApT], d[ApA], d[CpC], and d[GpT] as almost single peaks in HPLC analysis. Similarly, d[ApApApT] and d[CpCpCpT] were successfully synthesized without significant side reactions. Finally, d[CpCpCpCpCpCpT] and d[ApApApApApApT] were obtained as the main products. In the case of a longer oligomer, d[CpApGpTpCpApGpTpCpApGpT], a mixed solvent of CH(3)CN-N-methylpyrrolidone (1:1, v/v) was superior to THF so that the desired oligodeoxynucleotide could be isolated in a satisfactory yield. These results suggest that DNA synthesis can be carried out simply by using the protonated bases at the oligomer level not only without base protection but also without the capping reaction and the posttreatment of branched chains with MeOH-benzimidazolium triflate that previously was requisite. It is concluded that most of the reactions and solvent effects involved in this strategy can be explained in terms of simple acid-base reactions. Some problems associated with the previous posttreatment are also discussed with our own results.

Synthesis of the tRNA(Lys,3) anticodon stem-loop domain containing the hypermodified ms2t6A nucleoside

The synthesis of a protected form of the hypermodified nucleoside, N-[(9-beta-D-ribofuranosyl-2-methylthiopurin-6-yl)carbamoyl]threonine, (ms2t6A) is reported. The hypermodified nucleoside was subsequently elaborated to the protected nucleoside phosphophoramidite using a protecting group strategy compatible with standard RNA oligonucleotide chemistry. The phosphoramidite reagent was then used to synthesize the 17-nucleotide RNA hairpin having the sequence of the anticodon stem-loop (ASL) domain of human tRNA(Lys,3), the primer for HIV-1 reverse transcriptase. Introduction of the modification at position 37 of the tRNA ASL modestly decreases the thermodynamic stability of the RNA hairpin as has been seen previously for the prokaryotic t6A nucleoside lacking the 2-methylthio substituent. 2D NOESY NMR spectra of the ms2t6A containing tRNA ASL indicate that the threonyl side chain adopts a conformation similar to that seen in the solution structure of the analogous t6A containing E. coli tRNA(Lys), despite the presence of the bulky methylthio group. This synthetic approach allows for site-specific incorporation of the hypermodified nucleoside and should facilitate future studies directed at understanding the roles of nucleoside modification in modulating the stability and specificity of biologically important RNA-RNA interactions. Our synthesis of the ms2t6A containing RNAs demonstrates that this methodology is suitable for obtaining quantities of RNA required for structural studies of the HIV primer tRNA.

Chemical synthesis of a messenger ribonucleic acid fragment: AUGUUCUUCUUCUUCUUC

The synthesis via a phosphotriester method of the octadecaribonucleotide AUG(UUC)5 (19) is reported. The octadecanucleotide is meant to serve as a synthetic messenger in a ribosomal protein synthesizing system. A fully protected octadecamer intermediate (18a) was prepared by a block coupling procedure. For the introduction of the desired 3'-5'-internucleotide bonds a 3'-O-(2,2,2-trichloroethyl 2-chlorophenyl phosphate) function was incorporated into the monomeric building blocks which were applied in the synthesis of 18a. Monomeric and oligomeric compounds with a thus protected 3'-O-phosphotriester function can be selectively deblocked to give 3'-O-phosphodiester derivatives suitable for condensation with 5'-hydroxyl (oligo)nucleotides. Conversion of fully protected oligomers to 5'-hydroxyl derivatives, suitable for further coupling at the 5' end, was effected by selective removal of the levulinyl function at the 5' end. The fully protected octadecanucleotide 18a was deblocked with fluoride ions, followed by ammonia and acid to give the required octadecamer 19. The condensing agent 1-(2,4,6-triisopropyl-phenylsulfonyl)-3-nitro-1,2,4-triazole, which was applied to effect the formation of fully protected 3'-5'-internucleotide phosphotriester functions, may give rise to side reactions with the heterocylic bases uracil and guanine. The consequences of these side reactions for the synthesis of octadecamer 19 are reported.

The chemical synthesis of oligoribonucleotides VII. A comparison of condensing agents in the coupling of silylated ribonucleosides

The t-butyldimethylsilyl group is shown to be an ideal protecting group for the 2T-hydroxyl function of ribonucleosides during the synthesis of ribonucleotides using any of nine commonly used condensing agents. The phosphite coupling procedure compares favorably with all of the widely used condensing agents and provides a most convenient route to the key intermediates in the "modified" triester strategy.

Chromatography on Sephadex LH20 as an efficient purification step after removal of internucleotide 2,2,2-trichloroethyl protective groups from oligoribonucleotide phosphotriesters

Chromatography on Sephadex LH20, in a linear gradient of methanol in 0.02M TEAB buffer pH 7.5, is proposed as a fast and efficient method for the isolation and purification of protected oligoribonucleotide phosphodiesters obtained by deprotection of internucleotide phosphotriesters, and for the monitoring of the deprotection step itself. Its utility is shown on the example of removal of 2,2,2-trichloroethyl groups from oligoribonucleotide phosphotriester I of sequence CCCAUAA by two methods: /1/ reductive elimination with zinc in the presence of acetylacetone modified as presented here, and /2/ hydrogenolytic dehalogenation over palladium in pyridine. This method of chromatography on Sephadex LH20 is used as a key purification step during the removal of 2,2,2-trichloroethyl groups from I by method /1/ and allows to raise the yield of III during fianl deprotection step from 5 to 65%.