title: pH-Independent triplex formation: hairpin DNA containing isoguanine or 9-deaza-9-propynylguanine in place of protonated cytosine.
abstract: Triplex-forming oligonucleotides (TFOs) containing 2'-deoxyisoguanosine (2), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) as well as the propynylated 9-deazaguanine N7-(2'-deoxyribonucleoside) were prepared. For this the phosphoramidites 9a, b of the nucleoside 1 and, the phosphoramidites 19, 20 of compound 3b were synthesized. They were employed in solid-phase oligonucleotide synthesis to yield the protected 31-mer oligonucleotides. The deblocking of the allyl-protected oligonucleotides containing 1 was carried out by Pd(0)[PPh3]4-PPh3 followed by 25% aq. NH3. Formation of the 31-mer single-stranded intramolecular triplexes was studied by UV-melting curve analysis. In the single-stranded 31-mer oligonucleotides the protonated dC in the dCH(+)-dG-dC base triad was replaced by 2'-deoxyisoguanosine (1), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) and, 9-deaza-9-propynylguanine N7-(2'-deoxyribonucleoside) (3b). The replacement of protonated dC by compounds 1 and 3b resulted in intramolecular triplexes which are formed pH-independently and are stable under neutral conditions. These triplexes contain "purine" nucleosides in the third pyrimidine rich strand of the oligonucleotide hairpin.
authors.affiliation: Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany. Frank.Seela@uni-osnabrueck.de
authors.forename: Frank
authors.initials: F
authors.lastname: Seela
authors.forename: Khalil I
authors.initials: KI
authors.lastname: Shaikh
mesh_terms: D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000138:chemical synthesis* / Q000737:chemistry* / Q000235:genetics; D006147:Guanine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D008970:Molecular Weight; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000235:genetics; D011522:Protons; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D044366:Transition Temperature
chemical_list: C522197:9-deaza-9-propynylguanine; D009841:Oligonucleotides; D011522:Protons; C051802:triplex DNA; D006147:Guanine; C076777:9-deazaguanine; D003596:Cytosine; D004247:DNA; C008183:isoguanine