pH-Independent triplex formation: hairpin DNA containing isoguanine or 9-deaza-9-propynylguanine in place of protonated cytosine

Org Biomol Chem. 2006 Nov 7;4(21):3993-4004. doi: 10.1039/b610930f. Epub 2006 Oct 2.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chromatography, High Pressure Liquid
  • Cytosine / chemistry*
  • DNA / chemical synthesis*
  • DNA / chemistry*
  • DNA / genetics
  • Guanine / analogs & derivatives*
  • Guanine / chemical synthesis
  • Guanine / chemistry
  • Hydrogen-Ion Concentration
  • Magnetic Resonance Spectroscopy
  • Molecular Sequence Data
  • Molecular Weight
  • Nucleic Acid Conformation*
  • Oligonucleotides / chemical synthesis
  • Oligonucleotides / chemistry
  • Oligonucleotides / genetics
  • Protons*
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Transition Temperature

Substances

  • 9-deaza-9-propynylguanine
  • Oligonucleotides
  • Protons
  • triplex DNA
  • Guanine
  • 9-deazaguanine
  • Cytosine
  • DNA
  • isoguanine