Synthesis Of Thymidine Dimers Research Articles

Synthesis of Thymidine Dimers from 5′-O-Aminothymidine

The synthesis of modified oligonucleotides is of great importance for various therapeutic and diagnostic applications. The facile secondary structure formation of N-oxyamide-linked peptide analogues and the high nucleophilicity of the aminooxy function prompted us to prepare O-amino nucleoside derived dinucleosides. Herein, the efficient synthesis of three novel thymidine dimers with N-oxyamide, oxime and oxyamine linkages via a convergent approach from a common 5′-O-aminothymidine is reported.

RNA-Binding Affinities and Crystal Structure of Oligonucleotides Containing Five-Atom Amide-Based Backbone Structures,

Among the hundreds of nucleic acid analogues that have been studied over the last two decades only very few exhibit backbones with linkers between residues that are either shorter or longer than the four-atom linker O3'-P-O5'-C5' connecting sugar ring moieties in DNA and RNA. 2'-Deoxyribonucleoside dimers connected by a five-atom linker O3'-CH(CH(3))-CO-NH-CH(2) (*designates a chiral center) were reported to lead to only a slight destabilization of RNA-DNA hybrids in which the DNA strand contained one or several of these amide-linked dimers (De Napoli, L., Iadonisi, A., Montesarchio, D., Varra, M., and Piccialli, G. (1995) Synthesis of thymidine dimers containing a new internucleosidic amide linkage and their incorporation into oligodeoxyribonucleotides, Bioorg. Med. Chem. Lett. 5, 1647-1652). To analyze the influence of various chemistries of such five-atom amide linkers on the RNA-binding affinity of modified DNA strands, we have synthesized five different amide-linked dimers, including structures with homochiral linkers of the type X3'-C*H(CH(3))-CO-NH-CH(2) (X = O, CH(2)) as well as the corresponding analogues carrying methoxy groups at the 2'-position of the 3'-nucleosides. We have conducted a detailed thermodynamic analysis of duplex formation between the modified DNA and RNA, with the DNA strands containing between one and seven consecutive modified dimers. Some of the five-atom-linked dimers lead to significantly higher RNA-binding affinities compared with that of native DNA. Interestingly, the linkers with opposite stereochemistry at the chiral center stabilize duplexes between the modified DNA and RNA to different degrees. CD spectroscopy in solution and a crystal structure of an RNA-DNA duplex with a single amide-linked dimer demonstrate that the longer amide backbones do not disrupt the duplex geometry. These observations provide further evidence that stable cross-pairing between two different types of nucleic acids does not require the numbers of atoms linking their individual residues to match.

Incorporation of amide linked thymidine dimers into oligodeoxynucleotides

The synthesis of thymidine dimers in which the phosphodiester linkage has been replaced by an amide linkage containing diamines (homopiperazine, 2,5- trans-dimethylpiperazine, N, N-dimethylethylenediamine and N, N-diethylethylenediamine) and their incorporation into oligodeoxynucleotides is described. The thermal and nucleolytic stability of the resulting oligodeoxynucleotide analogues are reported.

Synthesis and Characterization of Short Oligonucleotide Segments Containing Nonnatural Internucleoside Amine- and Amide Linkages

Abstract The synthesis of thymidine dimers in which the phosphodiester linkage has been replaced by either piperazine or N,N'-dimethylethylenediamine are described. The dimers containing piperazine were incorporated into oligodeoxynucleotides on which thermal and enzymatic stability experiments were performed.

Synthesis of thymidine dimers containing piperazine in the internucleoside linkage and their incorporation into oligodeoxynucleotides

The synthesis of thymidine dimers in which the natural phosphodiester linkage has been replaced by piperazine (3′-(N(CH 2CH 2) 2N)-5′, 9 and 3′-(N(CH 2CH 2) 2N)-CO-4′, 10) are described. These new dimers were incorporated into oligodeoxynucleotides on an automated DNA-synthesizer using the phosphoramidite approach. The thermal stability of DNA/DNA duplexes and the enzymatic stability was studied by UV experiments. 17-Mers with 9 incorporated once or twice in the middle exhibited a pronounced decrease in thermal stability ( ΔT m∼−11 °C per modification) while 17-mers with 10 incorporated once or twice in the middle exhibited only a slight decrease in thermal stability ( ΔT m∼−2 δC per modification) when compared to unmodified 17-mers. Furthermore, end-modified oligodeoxynucleotides containing either 9 or 10 displayed five to six fold increased stability towards snake venom phosphodiesterase.

Synthesis of Oligodeoxyribonucleotides containing dimers with carbamate moieties as replacement of the natural phosphodiester linkage

The synthesis of thymidine dimers containing both possible regioisomeric carbamate moieties in place of the natural phosphodiester backbone is described. These dimers were incorporated in oligodeoxyribonucleotides and melting temperatures (T m) of the DNA/RNA and DNA/DNA duplexes are reported. In addition the nuclease resistance of these single strands were determined.