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'Parallel' and 'antiparallel' tail-clamps increase the efficiency of triplex formation with structured DNA and RNA targets

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http://hdl.handle.net/10256/26011

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Title:: 'Parallel' and 'antiparallel' tail-clamps increase the efficiency of triplex formation with structured DNA and RNA targets
Description:: Sequence-specific triple-helix structures can be formed by parallel and antiparallel DNA clamps interacting with single-stranded DNA or RNA targets. Single-stranded nucleic acid molecules are known to adopt secondary structures that might interfere with intermolecular interactions. We demonstrate the correlation between a secondary structure involving the target a stable stem predicted by in silico folding and experimentally confirmed by thermal stability and competition analyses and an inhibitory effect on triplex formation. We overcame structural impediments by designing a new type of clamp: 'tail-clamps'. A combination of gel-shift, kinetic analysis, UV thermal melting and thermodynamic techniques was used to demonstrate that tail-clamps efficiently form triple helices with a structured target sequence. The performance of parallel and antiparallel tail-clamps was compared: antiparallel tail-clamps had higher binding efficiencies than parallel tail-clamps both with structured DNA and RNA targets. In addition, the reported triplex-stabilizing property of 8- aminopurine residues was confirmed for tail-clamps. Finally, we discuss the possible use of this improved triplex technology as a new tool for applications in molecular biology
Origin:: © ChemBioChem, 2005, vol. 6, núm. 6, p. 1034-1042; Articles publicats (D-EQATA); Nadal i Matamala, Anna Eritja, Ramon Esteve Nuez, Teresa Pla i de Solà-Morales, Maria 2005 'Parallel' and 'antiparallel' tail-clamps increase the efficiency of triplex formation with structured DNA and RNA targets ChemBioChem 6 6 1034 1042
Idioma:: English
Relationship:: info:eu-repo/semantics/altIdentifier/doi/10.1002/cbic.200400358; info:eu-repo/semantics/altIdentifier/issn/1439-4227; info:eu-repo/semantics/altIdentifier/eissn/1439-7633
Author/Producer:: Nadal i Matamala, Anna; Eritja, Ramon; Esteve Nuez, Teresa; Pla i de Solà-Morales, Maria
Editor:: Wiley-VCH Verlag
Rights:: Tots els drets reservats; info:eu-repo/semantics/openAccess
Date:: 2005-06-06
Resource type:: info:eu-repo/semantics/article; info:eu-repo/semantics/acceptedVersion; peer reviewed
Format:: 9 p.; application/pdf

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2. < dc:creator > Nadal i Matamala, Anna </ dc:creator >
3. < dc:creator > Eritja, Ramon </ dc:creator >
4. < dc:creator > Esteve Nuez, Teresa </ dc:creator >
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6. < dcterms:abstract > Sequence-specific triple-helix structures can be formed by parallel and antiparallel DNA clamps interacting with single-stranded DNA or RNA targets. Single-stranded nucleic acid molecules are known to adopt secondary structures that might interfere with intermolecular interactions. We demonstrate the correlation between a secondary structure involving the target a stable stem predicted by in silico folding and experimentally confirmed by thermal stability and competition analyses and an inhibitory effect on triplex formation. We overcame structural impediments by designing a new type of clamp: 'tail-clamps'. A combination of gel-shift, kinetic analysis, UV thermal melting and thermodynamic techniques was used to demonstrate that tail-clamps efficiently form triple helices with a structured target sequence. The performance of parallel and antiparallel tail-clamps was compared: antiparallel tail-clamps had higher binding efficiencies than parallel tail-clamps both with structured DNA and RNA targets. In addition, the reported triplex-stabilizing property of 8- aminopurine residues was confirmed for tail-clamps. Finally, we discuss the possible use of this improved triplex technology as a new tool for applications in molecular biology </ dcterms:abstract >
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