title: Systematic optimization of ion-pairing agents and hexafluoroisopropanol for enhanced electrospray ionization mass spectrometry of oligonucleotides.
abstract: BACKGROUND
  New methods to enhance the electrospray ionization (ESI) signals are essential for low-level analysis of oligonucleotides. We report a systematic evaluation comparing 13 ion-pairing agents with and without hexafluoroisopropanol to understand their effect on the ion abundance of hetero-oligonucleotides.
  
  
  METHODS
  A Waters Synapt G2 HDMS quadrupole time-of-flight instrument was used to compare oligonucleotide signal intensity with 13 alkylamine ion-pairing agents at varying concentrations. The alkylamines that yielded the highest signal intensity were further evaluated with hexafluoroisopropanol at concentrations between 5 and 100 mM. The chemical properties of the solution components and analytes were evaluated to identify key factors in predicting optimal mobile phase conditions for different classes of oligonucleotides.
  
  
  RESULTS
  We identified a series of optimized mobile phase systems using diisopropylamine, tripropylamine, dimethylbutylamine, methyldibutylamine, and dimethylhexylamine along with 25 to 50 mM hexafluoroisopropanol that yielded significantly higher MS signal intensity for both siRNA and DNA compared with the traditionally used triethlyamine/hexafluoroisopropanol system. We explored charge state reduction, adduct formation and ESI mechanisms and identify the Henry's Law constant k aq/g as a key chemical property in predicting alkylamines that will increase oligonucleotide ion intensity. We also find that the hydrophobicity of the oligonucleotide plays a major role in choosing ion-pairing agents that will increase ion abundance.
  
  
  CONCLUSIONS
  This comprehensive and systematic optimization finds that the hydrophobicity of the oligonucleotide was a key factor in choosing alkylamine ion-pairing agents to increase ESI abundance. We identified that diisopropylamine and tripropylamine combined with lower concentrations of hexafluoroisopropanol yielded the highest signal intensity for these oligonucleotides.
authors.affiliation: Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, GA, 30602-2352, USA.
authors.forename: A Cary
authors.initials: AC
authors.lastname: McGinnis
authors.forename: E Claire
authors.initials: EC
authors.lastname: Grubb
authors.forename: Michael G
authors.initials: MG
authors.lastname: Bartlett
mesh_terms: D004247:DNA / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D020005:Propanols / Q000737:chemistry; D034741:RNA, Small Interfering / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000295:instrumentation* / Q000379:methods; D006845:Hydrocarbons, Fluorinated
chemical_list: D004247:DNA; D009841:Oligonucleotides; D020005:Propanols; D034741:RNA, Small Interfering; C001337:hexafluoroisopropanol; D006845:Hydrocarbons, Fluorinated