Document Detail


Double-stranded DNA-templated cleavage of oligonucleotides containing a P3'->N5' linkage triggered by triplex formation: the effects of chemical modifications and remarkable enhancement in reactivity.
MedLine Citation:
PMID:  20615902     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
We recently reported double-stranded DNA-templated cleavage of oligonucleotides as a sequence-specific DNA-detecting method. In this method, triplex-forming oligonucleotides (TFOs) modified with 5'-amino-2',4'-BNA were used as a DNA-detecting probe. This modification introduced a P3'→N5' linkage (P-N linkage) in the backbone of the TFO, which was quickly cleaved under acidic conditions when it formed a triplex. The prompt fission of the P-N linkage was assumed to be driven by a conformational strain placed on the linkage upon triplex formation. Therefore, chemical modifications around the P-N linkage should change the reactivity by altering the microenvironment. We synthesized 5'-aminomethyl type nucleic acids, and incorporated them into TFOs instead of 5'-amino-2',4'-BNA to investigate the effect of 5'-elongation. In addition, 2',4'-BNA/LNA or 2',5'-linked DNA were introduced at the 3'- and/or 5'-neighboring residues of 5'-amino-2',4'-BNA to reveal neighboring residual effects. We evaluated the triplex stability and reaction properties of these TFOs, and found out that chemical modifications around the P-N linkage greatly affected their reaction properties. Notably, 2',5'-linked DNA at the 3' position flanking 5'-amino-2',4'-BNA brought significantly higher reactivity, and we succeeded in indicating that a TFO with this modification is promising as a DNA analysis tool.
Authors:
Kosuke Ramon Ito; Tetsuya Kodama; Masaharu Tomizu; Yoshinori Negoro; Ayako Orita; Tomohisa Osaki; Noritsugu Hosoki; Takaya Tanaka; Takeshi Imanishi; Satoshi Obika
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2010-07-08
Journal Detail:
Title:  Nucleic acids research     Volume:  38     ISSN:  1362-4962     ISO Abbreviation:  Nucleic Acids Res.     Publication Date:  2010 Nov 
Date Detail:
Created Date:  2010-11-12     Completed Date:  2011-01-04     Revised Date:  2013-05-29    
Medline Journal Info:
Nlm Unique ID:  0411011     Medline TA:  Nucleic Acids Res     Country:  England    
Other Details:
Languages:  eng     Pagination:  7332-42     Citation Subset:  IM    
Affiliation:
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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MeSH Terms
Descriptor/Qualifier:
Base Pair Mismatch
Bridged Compounds / chemistry
DNA / chemical synthesis,  chemistry*
Hydrogen-Ion Concentration
Nitrogen / chemistry
Nucleic Acids / chemical synthesis,  chemistry
Phosphates / chemistry
Sequence Analysis, DNA*
Chemical
Reg. No./Substance:
0/Bridged Compounds; 0/Nucleic Acids; 0/Phosphates; 0/triplex DNA; 7727-37-9/Nitrogen; 9007-49-2/DNA
Comments/Corrections

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