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The chemical stability of abasic RNA compared to abasic DNA.

Küpfer PA, Leumann CJ - Nucleic Acids Res. (2006)

Bottom Line: We found that beta,delta-elimination was 154-fold slower compared to the same mechanism in abasic DNA.In the presence of aniline at pH 4.6, where only beta,delta-elimination contributes to strand cleavage, a 15-fold reduced cleavage rate at the RNA abasic site was observed.Thus abasic RNA is significantly more stable than abasic DNA.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

ABSTRACT
We describe the synthesis of an abasic RNA phosphoramidite carrying a photocleavable 1-(2-nitrophenyl)ethyl (NPE) group at the anomeric center and a triisopropylsilyloxymethyl (TOM) group as 2'-O-protecting group together with the analogous DNA and the 2'-OMe RNA abasic building blocks. These units were incorporated into RNA-, 2'-OMe-RNA- and DNA for the purpose of studying their chemical stabilities towards backbone cleavage in a comparative way. Stability measurements were performed under basic conditions (0.1 M NaOH) and in the presence of aniline (pH 4.6) at 37 degrees C. The kinetics and mechanisms of strand cleavage were followed by High pressure liquid chromotography and ESI-MS. Under basic conditions, strand cleavage at abasic RNA sites can occur via beta,delta-elimination and 2',3'-cyclophosphate formation. We found that beta,delta-elimination was 154-fold slower compared to the same mechanism in abasic DNA. Overall strand cleavage of abasic RNA (including cyclophosphate formation) was still 16.8 times slower compared to abasic DNA. In the presence of aniline at pH 4.6, where only beta,delta-elimination contributes to strand cleavage, a 15-fold reduced cleavage rate at the RNA abasic site was observed. Thus abasic RNA is significantly more stable than abasic DNA. The higher stability of abasic RNA is discussed in the context of its potential biological role.

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left: HPLC traces of strand cleavage via cyclophosphate formation and β,δ-elimination of 6b (0.1 M NaOH, 37°C) at different time intervals; controls: trace A: 6a, trace B: 6b, trace C: 6a (0.1 M NaOH, 6.5 h, 37°C), trace D: 6a (0.1 M NaOH, 6.5 h, 37°C, followed by photolysis); right: linear fit (R2 > 0.999) of ln[S]/[S0] versus t calculated from the HPLC traces.
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fig3: left: HPLC traces of strand cleavage via cyclophosphate formation and β,δ-elimination of 6b (0.1 M NaOH, 37°C) at different time intervals; controls: trace A: 6a, trace B: 6b, trace C: 6a (0.1 M NaOH, 6.5 h, 37°C), trace D: 6a (0.1 M NaOH, 6.5 h, 37°C, followed by photolysis); right: linear fit (R2 > 0.999) of ln[S]/[S0] versus t calculated from the HPLC traces.

Mentions: Since the two strand cleavage mechanisms studied separately so far act in concert in abasic RNA, it was necessary to study the effect of their combination on strand cleavage efficiency. For this purpose oligonucleotide 6b was subjected to 0.1 M NaOH and strand cleavage analyzed as described before (Figure 3).


The chemical stability of abasic RNA compared to abasic DNA.

Küpfer PA, Leumann CJ - Nucleic Acids Res. (2006)

left: HPLC traces of strand cleavage via cyclophosphate formation and β,δ-elimination of 6b (0.1 M NaOH, 37°C) at different time intervals; controls: trace A: 6a, trace B: 6b, trace C: 6a (0.1 M NaOH, 6.5 h, 37°C), trace D: 6a (0.1 M NaOH, 6.5 h, 37°C, followed by photolysis); right: linear fit (R2 > 0.999) of ln[S]/[S0] versus t calculated from the HPLC traces.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1761435&req=5

fig3: left: HPLC traces of strand cleavage via cyclophosphate formation and β,δ-elimination of 6b (0.1 M NaOH, 37°C) at different time intervals; controls: trace A: 6a, trace B: 6b, trace C: 6a (0.1 M NaOH, 6.5 h, 37°C), trace D: 6a (0.1 M NaOH, 6.5 h, 37°C, followed by photolysis); right: linear fit (R2 > 0.999) of ln[S]/[S0] versus t calculated from the HPLC traces.
Mentions: Since the two strand cleavage mechanisms studied separately so far act in concert in abasic RNA, it was necessary to study the effect of their combination on strand cleavage efficiency. For this purpose oligonucleotide 6b was subjected to 0.1 M NaOH and strand cleavage analyzed as described before (Figure 3).

Bottom Line: We found that beta,delta-elimination was 154-fold slower compared to the same mechanism in abasic DNA.In the presence of aniline at pH 4.6, where only beta,delta-elimination contributes to strand cleavage, a 15-fold reduced cleavage rate at the RNA abasic site was observed.Thus abasic RNA is significantly more stable than abasic DNA.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

ABSTRACT
We describe the synthesis of an abasic RNA phosphoramidite carrying a photocleavable 1-(2-nitrophenyl)ethyl (NPE) group at the anomeric center and a triisopropylsilyloxymethyl (TOM) group as 2'-O-protecting group together with the analogous DNA and the 2'-OMe RNA abasic building blocks. These units were incorporated into RNA-, 2'-OMe-RNA- and DNA for the purpose of studying their chemical stabilities towards backbone cleavage in a comparative way. Stability measurements were performed under basic conditions (0.1 M NaOH) and in the presence of aniline (pH 4.6) at 37 degrees C. The kinetics and mechanisms of strand cleavage were followed by High pressure liquid chromotography and ESI-MS. Under basic conditions, strand cleavage at abasic RNA sites can occur via beta,delta-elimination and 2',3'-cyclophosphate formation. We found that beta,delta-elimination was 154-fold slower compared to the same mechanism in abasic DNA. Overall strand cleavage of abasic RNA (including cyclophosphate formation) was still 16.8 times slower compared to abasic DNA. In the presence of aniline at pH 4.6, where only beta,delta-elimination contributes to strand cleavage, a 15-fold reduced cleavage rate at the RNA abasic site was observed. Thus abasic RNA is significantly more stable than abasic DNA. The higher stability of abasic RNA is discussed in the context of its potential biological role.

Show MeSH
Related in: MedlinePlus