DNA oligonucleotides

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Author(s) Barylyuk, Konstantin, Gülbakan, Basri, Xie, Xueshu, Zenobi, Renato
Publication Type Journal Items, Publication Status: Published
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Title DNA oligonucleotides
Subtitle A model system with tunable binding strength to study monomer-dimer equilibria with electrospray ionization-mass spectrometry
Author(s) Barylyuk, Konstantin
Gülbakan, Basri
Xie, Xueshu
Zenobi, Renato
Journal or Series Title Analytical chemistry
Volume Number 85
Issue Number 24
Start Page 11902
End Page 11912
ISSN 0003-2700
1520-6882
Publisher American Chemical Society
Publication Place Washington, D.C.
Publication Date 2013-12-17
Abstract Electrospray ionization (ESI) is increasingly used to measure binding strengths, but it is not always clear whether the ESI process introduces artifacts. Here we propose a model monomer-dimer equilibrium system based on DNA oligonucleotides to systematically explore biomolecular self-association with the ESI-mass spectrometry (MS) titration method. The oligonucleotides are designed to be self-complementary and have the same chemical composition and mass, allowing for equal ionization probability, ion transmission, and detection efficiency in ESI-MS. The only difference is the binding strength, which is determined by the nucleotide sequence and can be tuned to cover a range of dissociation constant values. This experimental design allows one to focus on the impact of ESI on the chemical equilibrium and to avoid the other typical sources of variation in ESI-MS signal responses, which yields a direct comparison of samples with different binding strengths. For a set of seven model DNA oligonucleotides, the monomer-dimer binding equilibrium was probed with the ESI-MS titration method in both positive and negative ion modes. A mathematical model describing the dependence of the monomer-to-dimer peak intensity ratio on the DNA concentration was proposed and used to extract apparent Kd values and the fraction of DNA duplex that irreversibly dissociates in the gas phase. The Kd values determined via ESI-MS titration were compared to those determined in solution with isothermal titration calorimetry and equilibrium thermal denaturation methods and were found to be significantly lower. The observed discrepancy was attributed to a greater electrospray response of dimers relative to that of monomers.
DOI 10.1021/ac402669e
Additional Notes Published online 14 November 2013
Document Type Article
Publication Status Published
Language English
NEBIS System Number 000005465
Source Database ID SCOPUS-84890444743
WOS-000328797200033
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@article{Brylyk2013,
  author = "Barylyuk, Konstantin and G{\"{u}}lbakan, Basri and Xie, Xueshu and Zenobi, Renato",
  title = "{D}{N}{A} oligonucleotides: {A} model system with tunable binding strength to study monomer-dimer equilibria with electrospray ionization-mass spectrometry",
  journal = "Analytical chemistry",
  year = 2013,
  volume = "85",
  number = "24",
  pages = "11902--11912",
  month = dec,
}


E-Citations record created: Tue, 21 Jan 2014, 07:36:44 CET