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“Parallel” and “Antiparallel Tail‐Clamps” Increase the Efficiency of Triplex Formation with Structured DNA and RNA Targets
Author(s) -
Nadal Anna,
Eritja Ramon,
Esteve Teresa,
Pla Maria
Publication year - 2005
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.200400358
Subject(s) - antiparallel (mathematics) , dna , rna , biophysics , nucleic acid , in silico , protein secondary structure , nucleic acid denaturation , molecular dynamics , nucleic acid secondary structure , intermolecular force , triple helix , thermal stability , chemistry , nucleic acid structure , crystallography , molecule , biology , biochemistry , stereochemistry , base sequence , computational chemistry , physics , organic chemistry , quantum mechanics , magnetic field , gene
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.