Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides.
Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine.
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, 119991, Russia.
N A
NA
Kolganova
A K
AK
Shchyolkina
A V
AV
Chudinov
A S
AS
Zasedatelev
V L
VL
Florentiev
E N
EN
Timofeev
D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D053837:DNA Cleavage; D015246:Deoxyribonuclease EcoRI / Q000378:metabolism; D061925:Immobilized Nucleic Acids / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry; D013696:Temperature
D061925:Immobilized Nucleic Acids; D009841:Oligonucleotides; C051802:triplex DNA; D004247:DNA; D015246:Deoxyribonuclease EcoRI