Backbone-modified oligonucleotides containing a butanediol-1,3 moiety as a ‘vicarious segment’ for the deoxyribosyl moiety—synthesis and enzyme studies

Wilk, Andrzej; Koziołkiewicz, Maria; Grajkowski, Andrzej; Uznański, Bogdan; Stec, Wojciech J.

doi:10.1093/nar/18.8.2065

Cited by 15 publications

(9 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…All these data testify that the EcoRII and MvaI enzymes interact with each of the bases of the central 'asymmetrical' A T-pair as well as with the outer and inner guanine residues of the recognition site. Similar results were obtained with EcoRI [18]. Replacement of any nucleoside residue of this enzyme recognition site by 1,3-butanediol residue blocks EcoRI action.…”

Section: Substrate Analogs Designsupporting

confidence: 80%

“…It is noteworthy that the ability to change the cleavage specificity and cut the substrate more effectively have been revealed only in the case of SsoII hydrolysis of substrates with non-nucleotide inserts. This phenomenon is not observed when duplexes II-VI, IX and X are cleaved by ScrFI, EcoRII and MvaI (see below), and when DNA duplexes with 1,3-butanediol residues in the EcoRI recognition site are cleaved by EcoRI [ 18]. What is the reason for such behaviour?…”

Section: Substrate Analogs Designmentioning

confidence: 99%

See 1 more Smart Citation

Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonucleaseSsoll

Кубарева

Petrauskene²,

Karyagina

et al. 1992

Nucl Acids Res

View full text Add to dashboard Cite

A study was made of the interaction between restriction endonucleases recognizing CCNGG (SsoII and ScrFI) or CCA/TGG (MvaI and EcoRII) DNA sequences and a set of synthetic substrates containing 1,3-propanediol, 1,2-dideoxy-D-ribofuranose or 9-[1'-hydroxy-2'-(hydroxymethyl)ethoxy] methylguanine (gIG) residues replacing either one of the central nucleosides or dG residues in the recognition site. The non-nucleotide inserts (except for gIG) introduced into the recognition site both increase the efficiency of SsoII and change its specificity. A cleavage at the noncanonical position takes place, in some cases in addition to the correct ones. Noncanonical hydrolysis by SsoII occurs at the phosphodiester bond adjacent to the point of modification towards the 5'-end. With the guanine base returned (the substrate with gIG), the correct cleavage position is restored. ScrFI specifically cleaves all the modified substrates. DNA duplexes with non-nucleotide inserts (except for the gIG-containing duplex) are resistant to hydrolysis by MvaI and EcoRII. Prompted by the data obtained we discuss the peculiarities of recognition by restriction endonucleases of 5-membered DNA sequences which have completely or partially degenerated central base pairs. It is suggested that SsoII forms a complex with DNA in an 'open' form.

show abstract

Section: Substrate Analogs Designsupporting

confidence: 80%

Section: Substrate Analogs Designmentioning

confidence: 99%

Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonucleaseSsoll

Кубарева

Petrauskene²,

Karyagina

et al. 1992

Nucl Acids Res

View full text Add to dashboard Cite

show abstract

“…l-RNA (van Boeckel et al, 1987;Ashley, 1992) and l/d-RNA dimers (Bhuta & Zemlicka, 1978) and their biological activities including resistance toward exonucleases have also been described. Also, recent studies with chimeric a-D-2'-deoxyribose/ci-D-2/-deoxyribose (Koga et al, 1991), acyclic/cyclic sugars (Wilk et al, 1990;Augustyns et al, 1991), D-hexose/D-deoxyribose (Augustyns et al, 1992), 2,-0-alkyl-D-ribose/2/-D-deoxyribose (Lesnik et al, 1993), and internucleotide linkage combinations of phosphodiesters with methyl phosphonates (Tidd & Warenius, 1989), phosphorothioate (Stein et al, 1988), formacetal (Matteucci, 1990), sulfide (Kawaietal., 1993), amide (Idziak et al, 1993;Mesmaeker et al, 1994), and other derivatives (for a recent review, see Yogesh and Cook (1993)) indicate beneficial nuclease resistance characteristics. One goal in this study was to incorporate L-2,-deoxyribonucleosides at multiple positions within a D-oligonucleotide chain and to evaluate the hybridization properties of such oligomers toward complementary DNA and RNA.…”

mentioning

confidence: 99%

Antisense L/D-Oligodeoxynucleotide Chimeras: Nuclease Stability, Base-Pairing Properties, and Activity at Directing Ribonuclease H

Damha¹,

Giannaris²,

Marfey³

1994

Biochemistry

View full text Add to dashboard Cite

Ultraviolet thermal denaturation studies substantiate our earlier hypothesis that substitution of a L-nucleotide residue for a D-nucleotide within a DNA duplex permits a stable structure in which all bases are paired through Watson-Crick hydrogen bonds (Damha, M. J., Giannaris, P. A., Marfey, P., & Reid, L. S. (1991) Tetrahedron Lett. 32, 2573-2576). This conclusion is also evident from the NMR work of Blommers et al. [Blommers, M. J. J., et al. (1994) Biochemistry (following paper in this issue)]. Our thermal denaturation studies indicate that, while weakening the interaction with target DNA and RNA, these substitutions allow for excellent cooperative binding. When the target is single-stranded DNA, the melting temperature of the complex is lowered by 4-5 degrees C per L-dU incorporation and by 0.4-2.6 degrees C when an internal D-dC is replaced by L-dC (1 M NaCl). When the target is RNA, the depression of Tm is also greater for L-dU substitutions (5-8 degrees C) than for L-dC substitutions (2-4 degrees C). The depressions of Tm caused by introducing A/C and G/T mismatches at the same positions were significantly greater. L/D-DNA chimeras were found to activate RNase H cleavage when hybridized to RNA. Furthermore, the stability of chimeric L/D-DNA against degradation by various commercial phosphodiesterases was found to be significant, as was their stability against digestion in human serum. These experiments establish that L/D-DNA chimeras serve as excellent models of antisense oligonucleotides.

show abstract

“…For 31P-NMR, 6 is given in ppm at 250 MHz. (11,12). The 1,2-dideoxyribose-3-cyanoethyl-phosphoramidite derivative 15 was synthesised according to described procedures (13,14) from commercial 2-deoxy-D-ribose.…”

Section: Resultsmentioning

confidence: 99%

Sterical recognition by T₄polynucleotide kinase of non-nucleosidic moieties 5′-attached to oligonucleotides

Fontanel

Bazin²,

Téoule

1994

Nucl Acids Res

View full text Add to dashboard Cite

The ability of T4 polynucleotide kinase (PNK) to phosphorylate non-nucleosidic moieties 5'-attached to oligodeoxynucleotides (ODNs) has been investigated. Non-nucleosidic phosphoramidite units were prepared from ethane-1,2-diol and propane-1,3-diol backbones. Some of them corresponded to pure enantiomers. They were used to obtain the corresponding 5'-end modified oligothymidylates X(pdT)10. The free primary hydroxyl of the non-nucleosidic moieties (X) of these oligomers was phosphorylated by PNK. We report the stereoselective phosphorylation of the L form of the 5'-end attached non-nucleosidic chiral fragments; the non-chiral moieties were completely phosphorylated. Dimers of glycerol analogue and thymidine 3'-phosphate were not recognized by PNK and the shortest modified ODN able to be phosphorylated was a trinucleotide X(pdT)3. A modified X(pdT)10, bearing a cyclic abasic site (X) at its 5'-end, was prepared by chemical synthesis from 1,2-dideoxyribose phosphoramidite and was phosphorylated with a 90% yield.

show abstract

Backbone-modified oligonucleotides containing a butanediol-1,3 moiety as a ‘vicarious segment’ for the deoxyribosyl moiety—synthesis and enzyme studies

Cited by 15 publications

References 7 publications

Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonucleaseSsoll

Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonucleaseSsoll

Antisense L/D-Oligodeoxynucleotide Chimeras: Nuclease Stability, Base-Pairing Properties, and Activity at Directing Ribonuclease H

Sterical recognition by T₄polynucleotide kinase of non-nucleosidic moieties 5′-attached to oligonucleotides

Contact Info

Product

Resources

About

Backbone-modified oligonucleotides containing a butanediol-1,3 moiety as a ‘vicarious segment’ for the deoxyribosyl moiety—synthesis and enzyme studies

Cited by 15 publications

References 7 publications

Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonucleaseSsoll

Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonucleaseSsoll

Antisense L/D-Oligodeoxynucleotide Chimeras: Nuclease Stability, Base-Pairing Properties, and Activity at Directing Ribonuclease H

Sterical recognition by T4polynucleotide kinase of non-nucleosidic moieties 5′-attached to oligonucleotides

Contact Info

Product

Resources

About

Sterical recognition by T₄polynucleotide kinase of non-nucleosidic moieties 5′-attached to oligonucleotides