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Oligonucleotide MS

Characterization Of Oligonucleotides

Why should you consider Novatia and ESI/LC/MS for your oligonucleotide characterization?

Novatia uses electrospray ionization liquid chromatography mass spectrometry (ESI/LC/MS) to characterize oligonucleotides. We can perform these analyses in a high-throughput mode to confirm the desired products from oligo synthesis reactions or in a more detailed mode using high resolution chromatographic separation. Most laboratories use MALDI-ToF and/or gel electrophoresis to characterize oligos. Novatia has developed the Oligo HTCS automated LC/MS system, which provides a number of advantages relative to MALDI-ToF and other traditional methods for oligo characterization.  Our methods are fast, cost-effective, and informative!

Features and Benefits of Novatia Oligo LC/MS Analysis Services:

  • Excellent mass accuracy, typically ± 0.01% for our standard ESI/MS analysis
  • Exact mass determination is also available with ppm-level (parts-per-million) accuracy on our high resolution mass spectrometers (orbitrap and QTof)
  • Mass resolution and accuracy much better than MALDI
  • High quality results for larger (>50 base) oligonucleotides
  • High throughput MW determination/confirmation
  • “Soft” ionization allows analysis of DMT-on and other oligos with labile chemical moieties
  • Detailed LC/UV/MS analysis for component profiling
  • ProMass ESI spectral deconvolution technology
  • Unique, easy-to-use, web-based results reports
  • Very attractive pricing!
  • Fast turnaround!  Results are typically returned the same or next day on most analyses.
  • We also specialize in protein LC/MS characterization.
  • Download the oligonucleotide MS analysis brochure.

Oligonucleotide Sequence Confirmation

Novatia uses a unique approach that utilizes high resolution mass spectrometry and novel deisotoping and charge deconvolution software for MS-based oligonucleotide sequencing.  The approach allows us to confirm oligonucleotide sequences from their MS/MS fragmentation patterns.

PEGylated Oligonucleotide Analysis

Novatia also has an LC/MS method for analyzing oligonucleotides that have been modified with PEG.

Oligonucleotide Metabolite Identification Analysis

Novatia can perform oligo metabolite identification on your therapeutic oligonucleotide compounds.  Samples (single stranded or duplexes) are incubated in biological matrices over a series of time points, as determined by the needs of the client application.  Samples are efficiently extracted to remove interfering background proteins and are analyzed by high-resolution mass spectrometry.  Novatia’s unique ProMass HR deconvolution software technology is then used to identify the metabolites found.  The disappearance of the parent compound(s) are also tracked over the time course.

NTP LCMS Analysis

Nucleoside triphosphates (NTPs), including chemically modified NTPs, are important compounds in cellular and molecular biology research.  Novatia uses a volatile ion pairing buffer that allows for high fidelity characterization of these compounds and their impurities by LC/UV/MS in the negative ion mode.  Analyses can be performed in either nominal or accurate mass analysis modes.