Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

Sarah E. Pierce, Junmei Wang, Janarthanan Jayawickramarajah, Andrew Hamilton, Jennifer S. Brodbelt

Research output: Contribution to journalArticle

Abstract

Isoguanine (2-oxo-6-aminoguanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads.

Original languageEnglish (US)
Pages (from-to)11244-11255
Number of pages12
JournalChemistry - A European Journal
Volume15
Issue number42
DOIs
StatePublished - Oct 26 2009

Fingerprint

Guanine
Cations
Positive ions
Annealing
Electrospray ionization
Mass spectrometry
Circular dichroism spectroscopy
Salt removal
isoguanine
Oligonucleotides
Dichroism
Ammonium Compounds
Isomers
Ion exchange
DNA
Gases
Association reactions
Ions

Keywords

  • Dna structures
  • Isoguanine
  • Mass spectrometry
  • Supramolecular chemistry

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats. / Pierce, Sarah E.; Wang, Junmei; Jayawickramarajah, Janarthanan; Hamilton, Andrew; Brodbelt, Jennifer S.

In: Chemistry - A European Journal, Vol. 15, No. 42, 26.10.2009, p. 11244-11255.

Research output: Contribution to journalArticle

Pierce, Sarah E. ; Wang, Junmei ; Jayawickramarajah, Janarthanan ; Hamilton, Andrew ; Brodbelt, Jennifer S. / Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats. In: Chemistry - A European Journal. 2009 ; Vol. 15, No. 42. pp. 11244-11255.
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