Clarity (SPE) Sample Preparation Information

Isolation and Purification of Synthetic Oligonucleotides

The Clarity BioSolutions sample preparation portfolio is composed of unique solid phase extraction chemistries packed in 96-well plate and cartridge formats designed to efficiently and effectively purify oligonucleotides.

Works for desalting and clean-up of biological samples
Specially formulated buffers solutions available for optimal performance
Quick protocols for rapid results

Clarity BioSolutions Product Selection

Purification

	Clarity QSP™	Clarity Oligo-RP™ Clarity Oligo-XT	Clarity Oligo-SAX™	Clarity RP-Desalting™
Primary Use	High-throughput, trityl-on RPC purification	RP-HPLC purification of failure sequences from target sequences	Economical, high loading capacity IEX-LC prep-scale purification	Quick removal or salt & excess reagent
Purities	>90%	>90%	>90%	~70%
Recoveries	~90%	~70%	>90%	~70%
Synthesis Scale Load	Up to 50 µmol	Up to 50 µmol	Up to 50 µmol	Up to 1 µmol
Oligo Types	DNA, RNA/RNAi, Thioates, Dye-labled, Modified

Characterization / Analysis

	Clarity Oligo-RP™	Clarity Oligo-MS™ Clarity Oligo-XT	Clarity Oligo-OTX™
Primary Use	RP-LC-MS analysis with optimized selectivity and sensitivity	Rapid, high efficiency RP-LC-MS analysis for QC and characterization	Extraction of oligo therapeutics from biological samples for LC-MS bioanalysis
Oligo Length	≤ 60 mer	≤ 60 mer	≤ 40 mer
Recommended Mobile Phase	TEA / HFIP	TEA/HFIP/MeOH	N/A

Material Characteristics

Clarity Products	Particle Support	Bonded Phase	Particle shape/Size (µm)	Pore Size (Å)	Surface Area (m²/g)
Clarity QSP™ Cartridges	Polymer (PSDVB)	Hydrophilic polymer coating	35	500	300
Clarity Oligo-RP™ LC Columns	TWIN (silica, organic, composite)	C18	3, 5, 10	110	375
Clarity Oligo-WAX™ LC Columns	Silica	Crosslinked polyamine (WAX)	10	360	−
Clarity RP-Desalting™ Tubes	Silica	C18	55	140	300
Clarity Oligo-MS™ LC Columns	Core-Shell	C18	1.7, 2.6, 5	100	200* (*effective)
Clarity OTX™ Extraction Plates	Polymer (surface modified PSDVB)	Mixed-mode anion exchanger	33	85	800
Clarity Oligo-SAX LC Columns	Polymer (surface modified PSDVB)	Hydrophilic quaternary amine	5	−	−
Clarity Oligo-XT LC Columns	Core-Shell	C18	1.7, 2.6, 5	100	200

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<div id="clarityspepage">
<h3 style="color: #000">Isolation and Purification of Synthetic Oligonucleotides</h3>

<p>The Clarity BioSolutions sample preparation portfolio is composed of unique solid phase extraction chemistries packed in 96-well plate and cartridge formats designed to efficiently and effectively purify oligonucleotides.</p>

<ul>
	<li>Works for desalting and clean-up of biological samples</li>
	<li>Specially formulated buffers solutions available for optimal performance</li>
	<li>Quick protocols for rapid results</li>
</ul>

<div class="clarsperow">
<h3>Clarity BioSolutions Product Selection</h3>

<div class="clarsperow">
<h4>Purification</h4>

<table class="clarityspe-purification">
	<tbody>
		<tr>
			<th> </th>
			<th>Clarity QSP™</th>
			<th>Clarity Oligo-RP™<br />
			Clarity Oligo-XT</th>
			<th>Clarity Oligo-SAX™</th>
			<th>Clarity RP-Desalting™</th>
		</tr>
		<tr>
			<td style="text-align: left">Primary Use</td>
			<td>High-throughput, trityl-on RPC<br />
			purification</td>
			<td>RP-HPLC purification of failure<br />
			sequences from target sequences</td>
			<td>Economical, high loading capacity<br />
			IEX-LC prep-scale purification</td>
			<td>Quick removal or salt & excess reagent</td>
		</tr>
		<tr>
			<td style="text-align: left">Purities</td>
			<td>>90%</td>
			<td>>90%</td>
			<td>>90%</td>
			<td>~70%</td>
		</tr>
		<tr>
			<td style="text-align: left">Recoveries</td>
			<td>~90%</td>
			<td>~70%</td>
			<td>>90%</td>
			<td>~70%</td>
		</tr>
		<tr>
			<td style="text-align: left">Synthesis Scale Load</td>
			<td>Up to 50 µmol</td>
			<td>Up to 50 µmol</td>
			<td>Up to 50 µmol</td>
			<td>Up to 1 µmol</td>
		</tr>
		<tr>
			<td style="text-align: left">Oligo Types</td>
			<td colspan="4">DNA, RNA/RNAi, Thioates, Dye-labled, Modified</td>
			
		</tr>
		
	</tbody>
</table>

<h4>Characterization / Analysis</h4>

<table class="clarityspe-charac">
	<tbody>
		<tr>
			<th> </th>
			<th>Clarity Oligo-RP™</th>
			<th>Clarity Oligo-MS™<br />
			Clarity Oligo-XT</th>
			<th>Clarity Oligo-OTX™</th>
		</tr>
		<tr>
			<td style="text-align: left">Primary Use</td>
			<td>RP-LC-MS analysis with optimized<br />
			selectivity and sensitivity</td>
			<td>Rapid, high efficiency RP-LC-MS<br />
			analysis for QC and characterization</td>
			<td>Extraction of oligo therapeutics from<br />
			biological samples for LC-MS bioanalysis</td>
		</tr>
		<tr>
			<td style="text-align: left">Oligo Length</td>
			<td>≤ 60 mer</td>
			<td>≤ 60 mer</td>
			<td>≤ 40 mer</td>
		</tr>
		<tr>
			<td style="text-align: left">Recommended Mobile Phase</td>
			<td>TEA / HFIP</td>
			<td>TEA/HFIP/MeOH</td>
			<td>N/A</td>
		</tr>
		
	</tbody>
</table>

<h4>Material Characteristics</h4>

<table class="clarityspe-material">
	<tbody>
		<tr>
			<th>Clarity Products</th>
			<th>Particle<br />
			Support</th>
			<th>Bonded<br />
			Phase</th>
			<th>Particle<br />
			shape/Size<br />
			(µm)</th>
			<th>Pore Size<br />
			(Å)</th>
			<th>Surface<br />
			Area<br />
			(m<sup>2</sup>/g)</th>
		</tr>
		<tr>
			<td style="text-align: left"><a href="https://www.phenomenex.com/Products/SPDetail/Clarity%20(SPE)/QSP?phaseTab=true" target="_blank">Clarity QSP™ Cartridges</a></td>
			<td>Polymer (PSDVB)</td>
			<td>Hydrophilic polymer coating</td>
			<td>35</td>
			<td>500</td>
			<td>300</td>
		</tr>
		<tr>
			<td style="text-align: left"><a href="https://www.phenomenex.com/Products/HPLCDetail/Clarity/Oligo-RP" target="_blank">Clarity Oligo-RP™<br />
			LC Columns</a></td>
			<td>TWIN<br />
			(silica, organic, composite)</td>
			<td>C18</td>
			<td>3, 5, 10</td>
			<td>110</td>
			<td>375</td>
		</tr>
		<tr>
			<td style="text-align: left"><a href="https://www.phenomenex.com/Products/HPLCDetail/Clarity/Oligo-WAX?phaseTab=true">Clarity Oligo-WAX™<br />
			LC Columns</a></td>
			<td>Silica</td>
			<td>Crosslinked polyamine (WAX)</td>
			<td>10</td>
			<td>360</td>
			<td>−</td>
		</tr>
		<tr>
			<td style="text-align: left"><a href="https://www.phenomenex.com/Products/SPDetail/Clarity%20(SPE)/RP%20Desalting?phaseTab=true" target="_blank">Clarity RP-Desalting™ Tubes</a></td>
			<td>Silica</td>
			<td>C18</td>
			<td>55</td>
			<td>140</td>
			<td>300</td>
		</tr>
		<tr>
			<td style="text-align: left"><a href="https://www.phenomenex.com/Products/HPLCDetail/Clarity/Oligo-MS?phaseTab=true" target="_blank">Clarity Oligo-MS™<br />
			LC Columns</a></td>
			<td>Core-Shell</td>
			<td>C18</td>
			<td>1.7, 2.6, 5</td>
			<td>100</td>
			<td>200*<br />
			(*effective)</td>
		</tr>
		<tr>
			<td style="text-align: left"><a href="https://www.phenomenex.com/Products/SPDetail/Clarity%20(SPE)/OTX?phaseTab=true" target="_blank">Clarity OTX™<br />
			Extraction Plates</a></td>
			<td>Polymer (surface<br />
			modified PSDVB)</td>
			<td>Mixed-mode anion exchanger</td>
			<td>33</td>
			<td>85</td>
			<td>800</td>
		</tr>
		<tr>
			<td style="text-align: left"><a href="https://www.phenomenex.com/Products/HPLCDetail/Clarity/Oligo-SAX?phaseTab=true">Clarity Oligo-SAX<br />
			LC Columns</a></td>
			<td>Polymer (surface<br />
			modified PSDVB)</td>
			<td>Hydrophilic quaternary amine</td>
			<td>5</td>
			<td>−</td>
			<td>−</td>
		</tr>
		<tr>
			<td style="text-align: left"><a href="https://www.phenomenex.com/Products/HPLCDetail/Clarity/Oligo-XT?phaseTab=true" target="_blank">Clarity Oligo-XT<br />
			LC Columns</a></td>
			<td>Core-Shell</td>
			<td>C18</td>
			<td>1.7, 2.6, 5</td>
			<td>100</td>
			<td>200</td>
		</tr>
		
	</tbody>
</table>
</div>
</div>
</div>

3 Phases

Reversed Phase 2

Ion-Exchange 1

Featured

BROCHURE

High-Throughput Synthetic DNA/RNA Purification

Developed to be a versatile, gentle, and extremely effective trityl-on purification process, Clarity QSP 96-well plates and cartridges deliver near impurity-free, concentrated full-length sequences.
BROCHURE

Extraction of Oligo Therapeutics from Biological Samples for LC/MS Bioanalysis

Clarity OTX is a simple, rapid, and reproducible solution that efficiently extracts oligos from biological matrices and can be easily automated.
TECHNICAL NOTE

Avoiding Depurination During Trityl-On Purification

Using Clarity QSP cartridges, we were able to substantially minimize if not eliminate depurination from occurring during purification.
TECHNICAL NOTE

Comparing Performance of High-Throughput, Trityl-On RNA/DNA Purification Products

Clarity QSP cartridges provide ease and efficacy not typically found in competing trityl-on purification platforms, such as the *TOP™ products.

RP Desalting Phase Detail

RP Desalting Phase Information

Quick Salt Removal

Clarity RP-Desalting™ tubes utilize reversed phase, in lieu of size exclusion, to eliminate salt and reagent from trityl-off synthetic oligo mixtures in order to capitalize on the speed and loading capacity benefits.

~70 % purity and ~80 % recovery of target oligo
Economical and disposable format

Desalting of Dye-Labeled DNA

A quencher-labeled sample of DNA (25nt) with the sequence FAMTTGACTTAGACTTAGA-CTTAGTTT was desalted using Clarity RP-Desalting tubes in the 200 mg/3 mL format. Collection fractions were then analyzed for purity and recovery using the above protocol.

}
	
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<div id="clarityrp-desalt">
<h3>Quick Salt Removal</h3>

<p>Clarity RP-Desalting™ tubes utilize reversed phase, in lieu of size exclusion, to eliminate salt and reagent from trityl-off synthetic oligo mixtures in order to capitalize on the speed and loading capacity benefits.</p>

<ul>
	<li>~70 % purity and ~80 % recovery of target oligo</li>
	<li>Economical and disposable format</li>
</ul>

<div class="rpsaltrow" style="padding-top: 3px">
<h4>Desalting of Dye-Labeled DNA</h4>
<a href="https://www.phenomenex.com/Application/Detail/15991" target="_blank"><img src="https://www.phenomenex.com/webimage/19clarity_rp-desalt_app15991.png" /></a>

<div>
<p class="app15991">A quencher-labeled sample of DNA (25nt) with the sequence FAMTTGACTTAGACTTAGA-CTTAGTTT was desalted using Clarity RP-Desalting tubes in the 200 mg/3 mL format. Collection fractions were then analyzed for purity and recovery using the above protocol.</p>
</div>
</div>
</div>

3 Phases

Reversed Phase 2

Ion-Exchange 1

Technical Documents
Search FAQ

Document Type:

Document Type	Title
Technical Notes	Automated Method Development of Oligonucleotide in Tissues Using Clarity OTX 96-Well Plate and High Resolution Mass Spectrometry (TN-0097)	Add to My Documents
Brochures	Clarity Biosolutions for Synthetic DNA/RNA	Add to My Documents
Brochures	Clarity OTX Application Guide	Add to My Documents
Supporting Docs	Clarity Overview Flyer	Add to My Documents
Brochures	Clarity QSP	Add to My Documents
Technical Notes	Extraction of 2’-MOE Phosphorothioate from Plasma Using Clarity OTX	Add to My Documents
Technical Notes	Extraction of 2’-MOE Phosphorothioate from Tissue Using Clarity OTX Solid Phase Extraction (SPE)	Add to My Documents
Other	Method Development Webinar Poster	Add to My Documents
Brochures	Sample Preparation Accessories	Add to My Documents
Other	Sample Preparation Reference Manual & Users Guide	Add to My Documents
Technical Notes	Avoiding Depurination During Trityl-on Purification (TN-0008)	Add to My Documents
Brochures	Clarity OTX	Add to My Documents
Supporting Docs	Clarity OTX Solid Phase Extraction Overview	Add to My Documents
Supporting Docs	Clarity OTX User Guide	Add to My Documents
Supporting Docs	Clarity QSP User’s Guide (DNA)	Add to My Documents
Supporting Docs	Clarity QSP User’s Guide (RNA)	Add to My Documents
Technical Notes	Trityl-on RNA and DNA Purification (TN-0009)	Add to My Documents
Supporting Docs	FAQs for the Isolation and Purification of Synthetic Oligonucleotides	Add to My Documents
Supporting Docs	Oligonucleotide Analysis: Experience the Power of Ultra-High Recoveries and Best-in-Class Specificity	Add to My Documents
Technical Notes	Oligonucleotide Therapeutics from Biological Matrices (TN-0048)	Add to My Documents
Supporting Docs	Collection Plate and Sealing Mat Selection Guide	Add to My Documents
Other	Protein and Peptide Users Guide	Add to My Documents
Brochures	Clarity Biosolutions for Synthetic DNA/RNA - Japanese	Add to My Documents
Technical Notes	RNA Sample Preparation and High Throughput Purification for TBDMS and TOM Chemistries (TN-0016)	Add to My Documents
Supporting Docs	SPE 10, 12, and 24 Position Vacuum Manifold Instructions	Add to My Documents
Supporting Docs	SPE 96-Well Vacuum Manifold	Add to My Documents

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