Rational Design of Switched Triple Helix-Forming Oligonucleotides: Extension of Sequences for Triple Helix Formation

摘要

A rational design by means of molecular mechanics has been carried out in an effort to extend the range of double-helical DNA sequences that could be recognized by triple helix-forming oljgonucleotides. The DNA target is composed of alternating, adjacent fragments of otigopurine-oligopyrimidine sequences, instead of a long stretch of polypurine-polypyrimidine sequence used for canonical triple helix formation. Based on the combination of different triple helix motifs in either Hoogsleen or reverse Hoogsteen configuration, mini-triple helices can be formed at each origopurine oligopyrimidine part of the target sequence with either parallel or antiparallel orientation with respect to the purine strand. As the adjacent purine target sequences are located in the complementary strands, the third strand oligonucleotides can be joined together through a natural phosphodiester backbone at the junctions in either a 5'-3' or a 3'-5' polarity. There are six distinct junction steps. Molecular modeling was aimed at optimizing the cooperative binding of the so-called switched triple helix-forming oligonucleotides by choosing appropriate nucleotide(s) at the junction between two adjacent mini-triple helices. A comprehensive switch code describing the rules for forming switched triple helices has been established. Its practical applications in extending DNA recognition by this new generation of tailor-made triple helix-forming oligonucleotides are discussed.