Yao-Zhong Xu

Synthesis by post-synthetic substitution of oligomers containing guanine modified at the 6-position with S-, N-, O-derivatives

Abstract 6-(2,4-dinitrophenyl)thioguanine phosphoramidite monomers with the 2-amino group of the base protected by either the isobutyryl or phenylacetyl group were incorporated into oligodeoxynucleotides with an automatic DNA synthesizer. N 2 -protection with the isobutyryl group was unsatisfactory because of the difficulty of removing it after synthesis of the oligemer. However, post-synthetic conversion of the N 2 -phenylacetyl protected 6-(2,4-dinitrophenyl)thioguanine gives oligomers containing 6-thioguanine, 2,6-diaminopurine, 2-amino-6-methylaminopurine, O 6 -methylguanine or guanine in high yield and purity. Potentially oligemers containing other labile functional groups at the 6-position could be produced by the procedure. DNA duplexes containing 6-thioguanine paired to cytosine had a markedly lower melting temperature (Tm) than counterparts containing G:C. However a DNA duplex containing 4-thiothymine paired to A had a Tm similar to that of a DNA duplex containing T:A. The distortion in DNA structure caused by 6-thioguanine may play a role in the biological effect of this compound.

Simple synthesis of 4-thiothymidine, 4-thiouridine and 6-thio-2′-deoxyguanosine

Abstract 4-triazolo-pyrimidine nucleosides and 6-O-(mesitylenesulfonyl)-2′-deoxyguanosine, when treated with thiolacetic acid at room temperature, gave the corresponding 4-thiopyrimidine nucleosides and 6-thio-2′-deoxyguanosine with high yields (86–93%). Possible mechanisms are discussed.

Chromatographic separation of oligodeoxynucleotides with identical length: Application to purification of oligomers containing a modified base

A general procedure is described for separation and purification of oligodeoxynucleotides of identical length but different base composition, in particular, of oligomers containing modified bases such as 4-substituted thymines and 6-substituted guanines, using an anion-exchange column (either Mono Q or NucleoPac). The modified oligomers can be well separated from the analogous oligomers containing unmodified thymine or guanine under the basic conditions of the chromatography. The effects of oligomer length, base composition, and lipophilicity on the separation are discussed. A general rule which can be used for prediction of the order of elution of different oligomers and for estimation of tautomeric form of a modified base in the oligomer is presented.

Post-synthetic introduction of labile functionalities onto purine residues via 6-methylthiopurines in oligodeoxyribonucleotides

Abstract Two methods are described for the preparation of oligodeoxynucleotides containing 6-methylthiopurine residues. 6-Methylthiopurine phosphoramidite (6) has been prepared and incorporated into oligomers. Methylation with methyl iodide of 6-thiopurine (or 6-thioguanine) in oligomers also exclusively produces oligomers containing 6-methylthiopurine (or 6-methylthioguanine). The methylthio group at defined purine residues in the deprotected oligomers can be oxidized selectively and converted at the final step into various functional groups including radioactive 35 S-thio group, a useful tag for cross-linking studies.

Reactive DNA: 6-methylsulphoxypurine used for site-specific and chemical crosslinking with cysteine and its peptide

Abstract A novel method is described for site-specific and chemical crosslinking of oligodeoxynucleotides containing 6-methylsulphoxypurine with cysteine or peptides containing cysteine. 6-Methylsulphoxy group on purine is stable in aqueous solution, but easily replaceable by the thiol group of cysteine and glutathione. A mechanism of the reaction is proposed, and potential applications are discussed with a focus on DNA-protein interactions.

Oligodeoxynucleotides containing O2-alkylthymine: Synthesis and characterization

Abstract simple procedures for preparation of O 2 -alkylthymidines and of their phosphoramidite monomers ( IV ) are described. These monomers have been successfully incorporated into DNA oligomers. The measurements of the melting temperature (Tm) of DNA duplexes show that O 2 -methylthymine preferentially pairs with guanine rather than with adenine.

Solid Phase Synthesis of Oligodeoxynucleotides Containing O6-Alkylguanine and O4-Alkylthymine

Abstract Solid phase synthesis of pure oligodeoxynucleotides containing O6alkylguanine and O4alkylthymine are described. 4-triazolothymine has been incorporated into oligomers and by choice of the appropriate alkoxide or of ammonia these oligomers can be deprotected and the triazolide converted into the O4-alkylthymine or 5-methylcytosine in a single step.

Synthesis and Characterization of DNA Containing O6-Carboxymethylguanine

Abstract O 6 -Carboxymethylguanine was formed in DNA treated with N -nitrosoglycocholic acid and believed to be implicated in human gastrointestinal and colorectal tumour. An efficient method is presented here for synthesis of oligodeoxynucleotides containing O 6 -carboxymethylguanine at pre-determined positions. The synthetic protocol also allows for production of oligomers containing O 6 -aminocarbonylmethylguanine. These guanine-modified oligomers have been fully characterized and could provide a useful tool for biological studies of these modified bases.

Preparation of Oligodeoxynucleotides Containing 6-Methylthiopurine Residues by Chemical Synthesis or Specific Methylation

Abstract Two methods (chemical synthesis and specific methylation) are described for the preparation of oligodeoxynucleotides containing 6-methylthiopurine residues. 6-Methylthiopurine phosphoramidite (6) is prepared and incorporated into oligomers. Methylation with methyl iodide of 6-thiopurine (or 6-thioguanine) in oligonucleotides also leads to exclusive production of 6-methylthiopurine (or 6-methylthioguanine) oligomers.

An Improved Post-Synthetic Substitution Approach for Synthesis of Oligodeoxynucleotides Containing Labile 4-Substituted Thymines

Abstract A simple procedure is described for the preparation of a versatile oligodeoxynucleotide which contains 4-phenylthiothymidine. This versatile oligomer has been successfully used for synthesis of oligonucleotides containing labile 5-methyl-N4, N4-ethanocytosine (7) or 4-azido-5-methyl-2-pyrimidinone-1-β-(2′-deoxyriboside) (8).