Characterization of the secondary structure of an oligonucleotide corresponding to the autocleavage site of a precursor RNA from bacteriophage T4

Hosaka, Hideo; Sakabe, Ichiro; Sakamoto, Kensaku; Niimi, Tatsuya; Yokoyama, Shigeyuki; Takaku, Hiroshi

doi:10.1016/0167-4781(94)90188-0

Cited by 4 publications

(2 citation statements)

References 30 publications

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“…In order to detect positions on the template at which the reverse transcriptase pauses or stops artefactually incubation controls were processed in parallel with the samples treated with RNases. Some of these stops are thought to be the result from spontaneous RNA hydrolysis, which occurs most frequently at pyrimidine–adenine phosphodiester bonds and may show intrinsic fragility of RNA at these sites [31]. Others are probably due to pausing of the reverse transcriptase in highly structured regions of the RNA template [26].…”

Section: Resultsmentioning

confidence: 99%

Secondary structure of the 5′‐region of PGY1/MDR1 mRNA

et al. 2000

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In order to identify the optimal target sites for antisense oligonucleotides in the human multiple drug resistance mRNA, the secondary structure of the 5P P-terminal part of this mRNA (nucleotides 1^678) was investigated. By using results of probing with ribonucleases T1, ONE and V1 and results of computer simulations, a model of the 5P P-region of the PGY1/MDR1 mRNA was built. The molecule is formed by three major domains comprising several hairpins separated by single-stranded fragments. The predicted single-stranded regions of the PGY1/MDR1 mRNA efficiently bind complementary oligonucleotides. ß 2000 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.

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Section: Resultsmentioning

confidence: 99%

Secondary structure of the 5′‐region of PGY1/MDR1 mRNA

et al. 2000

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“…The influence of the RNA sequence and secondary struc ture on the efficiency and specificity of cleavage was ex amined only for divalent metal ions. [5][6][7][8][9] The cleavage of phosphodiester bonds located in hairpin loops was stud ied in detail 5-7 since a hairpin is the main structural element of natural RNA and because of important bio logical functions of hairpin loops. 10-12 Among various RNA loops, bulge loops, i.e., RNA regions containing nucleotides that have no complementary bases in the op posite RNA strand are of special interest.…”

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confidence: 99%

Cleavage of RNA bulge loops by artificial RNases

2006

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Sensitivity of phosphodiester bonds in RNA bulge loops to cleavage by short cationic peptides and compounds based on 1,4 diazabicyclo[2.2.2]octane and its conjugates with imid azole was studied. Bulge loops containing from one to seven nucleotides were formed in RNA upon its hybridization with partially complementary oligodeoxyribonucleotides. The efficiency of RNA cleavage depends on the length of a bulge loop, the position of the cleaved phosphodiester bond in the loop, and the nature of the RNA binding fragment of chemical ribonuclease (1,4 diazabicyclo[2.2.2]octane or a cationic peptide). In the absence of Mg 2+ ions, the phosphodiester bond in the CA motif located in the apical position in 4 , 6 , or 7 membered loops is cleaved with the highest efficiency. In the presence of magnesium ions, the selectivity of RNA cleavage within bulge loops is substantially enhanced. In the case of 1,4 diaza bicyclo[2.2.2]octane based compounds, RNA is subjected to cleavage predominantly at the bonds in 4 , 6 , and 7 membered loops, whereas cleavage of other bonds is greatly suppressed.In recent years, numerous low molecular weight com pounds capable of cleaving RNA under physiological con ditions have been designed. 1-4 The RNA cleavage by these compounds occurs predominantly at the regions that are not involved in double stranded structures, such as various loops, single stranded regions, and junctions. The influence of the RNA sequence and secondary struc ture on the efficiency and specificity of cleavage was ex amined only for divalent metal ions. 5-9 The cleavage of phosphodiester bonds located in hairpin loops was stud ied in detail 5-7 since a hairpin is the main structural element of natural RNA and because of important bio logical functions of hairpin loops. 10-12 Among various RNA loops, bulge loops, i.e., RNA regions containing nucleotides that have no complementary bases in the op posite RNA strand are of special interest. These loops arrange the RNA tertiary structure, 13,14 serve as specific RNA protein interaction sites, 15 and form ribozyme ac tive sites. 16 RNA bulge loops are sensitive to cleavage by a wide range of compounds and are potential targets for antisense oligonucleotide based conjugates exhibiting site selective cleavage of RNA. Phosphodiester bonds within RNA bulge loops display a high sensitivity to cleavage by metal ions. 5,8,9 Bonds in most of RNA bulge loops or RNA:DNA complexes are cleaved by divalent metal ions, the bonds located at the 3´ side (in some cases, at the 5´ side) of each nucleotide in the loop being predominantly cleaved. 5In addition, bonds that are adjacent to the bulge loop but are involved in an RNA:DNA duplex were subject to cleavage. 5Earlier, 17 we have studied the sensitivity of phospho diester bonds in one to seven membered RNA bulge loops to cleavage by the 1,4 diazabicyclo[2.2.2]oc tane-histidine conjugate (compound ABL4C3), which cleaves RNA selectively at bonds in 4 and 7 membered loops in the presence of magnesium ions. In the present study, we carried out a comp...

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