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Product Information
Phase Detail
Clarity OTX
Clarity OTX solid phase extraction tubes allow for the isolation of RNA and DNA-based therapeutics

Clarity OTX

15 Minute Clean Up from Biological Samples

Isolate RNA and DNA-based therapeutics / metabolites from biological fluids and tissues in less time with Clarity OTX solid phase extraction (SPE) and buffer products.

  • No liquid-liquid extraction (LLE) required required
  • >80 % typical extraction recoveries
  • Optimized for LC-MS bioanalysis

U.S. Patent No. 7,119,145

Clarity (SPE)
Recommended Use
Extraction of RNA and DNA-based therapeutics/metabolites from biological fluids and tissues

General Extraction

Common Extraction Procedure (~180 minutes)

Common Extraction Procedure (~180 minutes)
Suitable for Most Oligo Therapeutics & Samples

Oligo types Sample Types
DNA Plasma
Aptamers Serum
RNAi/siRNA Urine
Thioates Tears
Lipid-conjugates Saliva

Extraction Protocol

Sample Pre-Treatment
  • Proteinase K digestion or homogenize
  • Mix 1-to-1 with Lysis-Loading buffer
Biological Fluids
  • Mix 1-to-1 with Lysis-Loading buffer

Extraction Protocol Step 1-4

Detect Low Dosage Levels

Due to the typical 80 % and greater recoveries of the parent oligonucleotide therapeutic and its metabolites, detection in the picomole range is possible. The TIC below illustrates detection of a dosage in this very sensitive range. Aliquots of 500 ng & 50 ng spiked into plasma were extracted using Clarity OTX to determine sensitivity limits. A TIC of the 500 ng load is shown below. The 14.3 minute peak corresponding to the 19mer P-S can be quantitated. While a peak is not observed for the TIC of the 50 ng load, using a XIC at m/z of 944 (the -7 charge state) one can still quantitate the oligonucleotide at very low levels.

Sensitivity Study in Plasma

Clarity 3 µm Oligo-RP C18
50 x 4.6 mm
Part No.:
Mobile Phase:
A: 50 mM TEAA, pH 7.5 / 5 % Acetonitrile
B: Methanol
A/B (90:10) to A/B (40:60) in 20 min
Flow Rate:
1 mL/ min
UV @ 260 nm
25nt DNA oligonucleotide

UV chromatograms of oligonucleotide extracted from liver tissue using Clarity OTX. The 19mer extracted phosphorothioate oligonucleotide was spiked with 10 µg of a oligonucleotide internal standard before analysis. The top two chromatograms represent different levels of the incubated P-S oligo. The bottom chromatogram is an external standard of equal amounts of the 19mer oligo and internal standard. Note the high recovery of the oligonucleotide and low level of plasma contaminants from the incubated samples.

Sensitivity Study in Live Tissue

Application 18872: Sensitivity Study in Live Tissue

The level of MS sensitivity is highly linked to the MS instrument and HPLC mobile phase used. Contact Phenomenex for questions about sensitivity levels achieved with Clarity OTX on various instruments with specific mobile phases.