Synthesis of decadeoxyribonucleotides containing 5-modified uracils and their interactions with restriction endonucleasesBglII,Sau3AI andMboI (Nucleosides and Nudeotides 82¹)

Abstract

Decadeoxyribonucleotides containing uracil, 5-bromouracil, 5-cyanouracil and 5-ethyluracil in recognition sequences of restriction endonucleases Bgl II, Sau 3AI, Mbo I were synthesized. Decanucleotides containing 5-bromouracil in place of thymine had essentially the same susceptibility to all the restriction endonucleases. Uracil-containing decanucleotides were however very resistant to attack. Decanucleotides containing 5-cyanouracil in the recognition sequence were strongly resistant to hydrolysis by Sau 3AI, but were hydrolysed by Bgl II and Mbo I as well as the parent decanucleotide. Decanucleotides containing 5-ethyluracil were strongly resistant to hydrolysis by Sau 3AI, but were partially resistant to hydrolysis by Bgl II and Mbo I.

Origins of Sequence Selectivity in Homologous Genetic Recombination: Insights from Rapid Kinetic Probing of RecA-mediated DNA Strand Exchange

“…As first observed in polymer studies, 26-29 the addition of methyl groups to the C5 position of pyrimidine bases in duplex DNAs comprised of oligonucleotides increases the thermal stability of the dsDNA. [30][31][32][33][34] In agreement with these studies, cursory thermal denaturation studies revealed that the intrinsic thermal stabilities of the dsDNA substrates increase in the following order: D17 < D0 < D16. The placement of the base substitutions on the O-strand was designed to maximize any potential impact by changing the relative stabilities of both the substrate (C·O) and Three A·T bp were replaced by G·T bp or three G·C bp were replaced by I·C bp to create dsDNA substrates D18 and D19, respectively (see Figure 3).…”

“…26,[28][29][30][31][32][33] Likewise, thymine (5-methyluracil) stabilizes duplexes relative to uracil. 27,32,34 Indeed, Wang and Kool noted that, in sequence contexts similar to those utilized here, addition of pyrimdine C5-methyl substituents always results in increased thermal stability. 34 The origin of this stabilizing methyl effect can be largely attributed to enhanced base stacking.…”

Synthesis and properties of small interfering RNA duplexes carrying 5-ethyluridine residues

“…The stabilization is similar to the one described for 5-methylU but smaller than that of 5-propynylU [18]. In contrast, the replacement of uracil by 5-ethyluracil in DNA has been described to produce a slight destabilization of the duplex [26,27].…”

“…In DNA, oligonucleotides carrying 2'-deoxy-5-ethyluridine have shown a high stability to exonucleases [28] and to several restriction endonucleases [26]. In RNA oligonucleotides the presence of 5-methyluridines induced a moderate increase on the stability of siRNA in human serum [18].…”

5‐Bromodeoxyuridine induces transcription of repressed genes with disruption of nucleosome positioning

“…In support of this, expression of the genomic STE2 gene regulated by the α2/Mcm1 complex was not affected by the addition of BrdU (data not shown). In addition, some DNA‐binding proteins and enzymes examined to date cannot functionally distinguish between 5‐bromouracil and thymine on DNA [29–32]. These results suggest that an unusual DNA conformation induced by BrdU is the primary cause of altered nucleosome positioning.…”