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GENEWIZ | Oligo Synthesis FAQs
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<h1>Oligo Synthesis FAQs</h1> </div> </div> <div class="container FAQs"> <div class="row"> </div> <div class="row"> <div class="NoBorder panel-group acc-v1 container" id='OLIGO-SYNTHESIS-FAQs'> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-1" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>What is the difference between the <em>Overnight DNA Oligos</em>, <em>Custom DNA & RNA Oligos</em>, and <em>Oligos Retained for Sanger</em> services?</div> </a> </div> <div id="QA-1" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> <p><a href="/en/Public/Services/Oligo/Oligo-Rapid-Synthesis"><em><strong>Overnight DNA Oligos</strong></em></a>: Standard (non-modified, desalted) DNA oligos nucleotides (ranging from 15-60 bases at 25 or 50 nmol) delivered in 1-2 business days with two priorities options:</p> <ul> <li><strong>Standard Priority</strong>: Orders are typically delivered by second business day</li> <li><strong>Expedited Priority</strong>: Orders within region-specific guidelines are delivered as fast as next business day</li> </ul> <p>Please click <a href="/en/Public/Services/Oligo/Oligo-Rapid-Synthesis">here</a> to learn more about our Overnight DNA Oligos service and for guidelines based on region, oligo length, and time of order.</p> <p><a href="/en/Public/Services/Oligo/Oligo-Flex-Synthesis"><em><strong>Custom DNA & RNA Oligos</strong></em></a>: Synthesis of custom-length oligos (5-150 bases) at 25 - 1000 nmol scales with a wide range of modifications available with HPLC, PAGE, and desalted purification options. Turnaround time starts at 4 business days, depending on scale and modification requirements.</p> <p><a href="/en/Public/Services/Oligo/Oligo-Retained-for-Sanger-Sequencing"><em><strong>Oligos Retained for Sanger</strong></em></a>: Order oligos for your Azenta Sanger sequencing order. Azenta will synthesize, dilute, and store the oligo on-site for up to 1 year.</p> </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-2" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>What oligo length can Azenta synthesize?</div> </a> </div> <div id="QA-2" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> The Azenta <em>Overnight DNA Oligos</em> service accepts standard, desalted primers between 15-60 bases. <br /> <br /> The Azenta <em>Custom DNA & RNA Oligos</em> service can synthesize oligos between 5-150 bases. </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-3" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>How does Azenta synthesize oligos?</div> </a> </div> <div id="QA-3" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> Oligos are chemically synthesized using the industry-standard, solid-phase phosphoramidite method. Oligos are synthesized through a series of coupling reactions in the 3' and 5' direction. </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-4" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>Does Azenta offer degenerate bases?</div> </a> </div> <div id="QA-4" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> <style type="text/css"> body { margin: 0; } .oligo-ssg-table { width: 350px; margin: 0 auto; text-align: center; border: 1px solid #000; border-collapse:collapse } .oligo-ssg-table tr { border: 1px solid #000; } .oligo-ssg-table th { width: 50%; border: 1px solid #000; padding: 3px; background: #ADD8E6; } .oligo-ssg-table td { border: 1px solid #000; padding: 3px; } </style> Yes, Azenta offers synthesis of oligos containing degenerate bases using the standard IUPAC base nomenclature. <br /> <br /> <table class="oligo-ssg-table"> <tbody> <tr> <th style="text-align: center;">IUPAC Code </th> <th style="text-align: center;">Base</th> </tr> <tr> <td>R</td> <td>A or G</td> </tr> <tr> <td>Y</td> <td>C or T</td> </tr> <tr> <td>M</td> <td>A or C</td> </tr> <tr> <td>K</td> <td>G or T</td> </tr> <tr> <td>S</td> <td>C or G</td> </tr> <tr> <td>W</td> <td>A or T</td> </tr> <tr> <td>H</td> <td>A, C, or T</td> </tr> <tr> <td>B</td> <td>C, G, or T</td> </tr> <tr> <td>V</td> <td>A, C, or G</td> </tr> <tr> <td>D</td> <td>A, G, or T</td> </tr> <tr> <td>N</td> <td>A, C, G, or T</td> </tr> </tbody> </table> </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-5" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>When will I receive my oligos?</div> </a> </div> <div id="QA-5" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> <p><em>Overnight DNA Oligos</em> orders are typically received within 1-2 business days. Please reference delivery times <a href="https://www.genewiz.com/en/Public/Services/Oligo/Oligo-Rapid-Synthesis">here</a>.</p> <p> <em><em><span style="color: black;">Custom DNA & RNA Oligos </span></em><span style="color: black;"></span></em><span style="color: black;">service ships orders in as few as 4 business days depending on the modifications or purifications requested. Please refer to your order for specific turnaround time information</span><em><span style="color: black;">.<br /> <br /> <em>Oligos Retained </em></span></em><span style="color: black;">for Sanger</span><span style="color: black;"> will be available for sequencing within 1-2 business days depending on the time the order is placed.</span></p> </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-6" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>Can I receive oligos in solution?</div> </a> </div> <div id="QA-6" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> <p>Overnight DNA Oligo orders can be delivered dry or formulated dry, wet, in water, or a selection of buffers, normalized to 50 or 100 uM for no additional charge. </p> <p>Custom DNA & RNA Oligo orders can only be delivered in dry format.</p> </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-7" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>What is the recommended reconstitution protocol?</div> </a> </div> <div id="QA-7" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> If primers arrive dry, we recommend briefly centrifuging the tube to ensure that the DNA is at the bottom of the tube. Resuspend the sample in a volume or concentration appropriate for your needs and vortex briefly to mix well. Let the sample sit for 1-2 minutes. Before use, vortex briefly again. <br><br> *Please note the reconstitution solution is dependent on downstream applications and that TE may interfere with various enzymatic reactions. </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-8" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>How should the oligos be stored?</div> </a> </div> <div id="QA-8" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> Dry oligos are stable and can be stored at -20°C for 1 year. Resuspended primers at higher concentrations (≥100 µM, in TE or water) are stable for 6 months at -20ºC. <br><br> *Please note that repeated freezing and thawing will reduce stability and shelf life. </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-9" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>What purification options does Azenta offer?</div> </a> </div> <div id="QA-9" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> <style type="text/css"> body { margin: 0; } .oligo-ssg-table-2 { margin: 0 auto; text-align: center; border: 1px solid #000; border-collapse:collapse } .oligo-ssg-table-2 tr { border: 1px solid #000; } .oligo-ssg-table-2 th { width: 25%; border: 1px solid #000; padding: 3px; background: #ADD8E6; } .oligo-ssg-table-2 td { border: 1px solid #000; padding: 3px; } </style> <table class="oligo-ssg-table-2"> <tbody> <tr> <th style="text-align: center;">Purification</th> <th style="text-align: center;">Lengths (nt)</th> <th style="text-align: center;">Purity</th> <th style="text-align: center;">Recommended Uses</th> </tr> <tr> <td>Desalted</td> <td>5-90</td> <td>>70%</td> <td>Standard sequencing and PCR primers</td> </tr> <tr> <td>PAGE</td> <td>11-150</td> <td>>90%</td> <td>Long oligos</td> </tr> <tr> <td>HPLC</td> <td>5-90</td> <td>>95%</td> <td>Modified oligos or oligos used in sensitive applications</td> </tr> </tbody> </table> </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-10" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>How much yield is expected for each scale?</div> </a> </div> <div id="QA-10" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> <style type="text/css"> body { margin: 0; } .oligo-ssg-table-3 { margin: 0 auto; text-align: center; border: 1px solid #000; border-collapse:collapse } .oligo-ssg-table-3 tr { border: 1px solid #000; } .oligo-ssg-table-3 th { width: 25%; border: 1px solid #000; padding: 3px; background: #ADD8E6; } .oligo-ssg-table-3 td { border: 1px solid #000; padding: 3px; } </style> Azenta synthesizes DNA oligos on a per-scale basis, which refers to the initial amount of material used in synthesis. Due to the inefficiency of the coupling reactions, yields are never equal to the initial amount of starting material. Yield is typically impacted by the nature and content of the sequence. Purification and modifications will also reduce the final yield delivered.<br /> <br /> <table class="oligo-ssg-table-3"> <tbody> <tr> <th style="text-align: center;"> Length (nt) </th> <th style="text-align: center;"> Scale </th> <th style="text-align: center;"> Purification </th> <th style="text-align: center;"> Target Yield* </th> </tr> <tr> <td rowspan="14">5-90</td> <td rowspan="2">25 nmol</td> <td>Desalted</td> <td>5 nmol</td> </tr> <tr> <td>HPLC</td> <td>2 nmol</td> </tr> <tr> <td rowspan="3">50 nmol</td> <td>Desalted</td> <td>10 nmol</td> </tr> <tr> <td>HPLC</td> <td>4 nmol</td> </tr> <tr> <td>PAGE</td> <td>2 nmol</td> </tr> <tr> <td rowspan="3">100 nmol</td> <td>Desalted</td> <td>20 nmol</td> </tr> <tr> <td>HPLC</td> <td>8 nmol</td> </tr> <tr> <td>PAGE</td> <td>4 nmol</td> </tr> <tr> <td rowspan="3">200 nmol</td> <td>Desalted</td> <td>50 nmol</td> </tr> <tr> <td>HPLC</td> <td>20 nmol</td> </tr> <tr> <td>PAGE</td> <td>10 nmol</td> </tr> <tr> <td rowspan="3">1 µmol</td> <td>Desalted</td> <td>300 nmol</td> </tr> <tr> <td>HPLC</td> <td>120 nmol</td> </tr> <tr> <td>PAGE</td> <td>60 nmol</td> </tr> <tr> <td rowspan="3">91-150</td> <td>100 nmol</td> <td>PAGE</td> <td>2 nmol</td> </tr> <tr> <td>200 nmol</td> <td>PAGE</td> <td>5 nmol</td> </tr> <tr> <td>1 µmol</td> <td>PAGE</td> <td>25 nmol</td> </tr> </tbody> </table> <br /> <center>* Guaranteed yield will be determined by the exact oligo length, scale, and purification, and will be shown on the oligo order receipt. Actual yield delivered will be ±10% of guaranteed yield.</center> </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-11" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>What types of fluorescent modifications does Azenta offer and are these compatible with my equipment?</div> </a> </div> <div id="QA-11" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> <style type="text/css"> body { margin: 0; } .oligo-ssg-table-4 { text-align: center; border: 1px solid #000; border-collapse:collapse } .oligo-ssg-table-4 tr { border: 1px solid #000; } .oligo-ssg-table-4 th { width: 20%; border: 1px solid #000; padding: 3px; background: #ADD8E6; } .oligo-ssg-table-4 td { border: 1px solid #000; } </style> <table class="oligo-ssg-table-4"> <tbody> <tr> <th style="text-align: center;">Dye</th> <th style="text-align: center;">Max Ex (nm)</th> <th style="text-align: center;">Max Em (nm)</th> <th style="text-align: center;">Color</th> <th style="text-align: center;">Compatible Quenchers</th> </tr> <tr> <td>6-FAM</td> <td>495</td> <td>520</td> <td>Green</td> <td><span style="text-align: center;">BHQ-1, BHQ-2, ECLIPSE, TAMRA, Dabcyl</span></td> </tr> <tr> <td>JOE</td> <td>520</td> <td>548</td> <td>Orange</td> <td>BHQ-1, ECLIPSE, Dabcyl, TAMRA</td> </tr> <tr> <td>TET™</td> <td>521</td> <td>536</td> <td>Orange</td> <td>BHQ-1, BHQ-2, ECLIPSE, TAMRA, Dabcyl</td> </tr> <tr> <td>HEX™</td> <td>520</td> <td>548</td> <td>Pink</td> <td>BHQ-1, BHQ-2, ECLIPSE, TAMRA, Dabcyl </td> </tr> <tr> <td>TAMRA</td> <td>544</td> <td>576</td> <td>Rose</td> <td>BHQ-2, ECLIPSE, Dabcyl </td> </tr> <tr> <td>ROX™</td> <td>576</td> <td>601</td> <td>Red</td> <td>BHQ-2, ECLIPSE </td> </tr> <tr> <td>Cy®5</td> <td>650</td> <td>670</td> <td>Violet</td> <td>BHQ-2 </td> </tr> <tr> <td>Cy®3</td> <td>550</td> <td>570</td> <td>Red</td> <td>BHQ-2, ECLIPSE</td> </tr> <tr> <td>TexasRed®</td> <td>583</td> <td>603</td> <td>Red</td> <td>BHQ-2, ECLIPSE</td> </tr> </tbody> </table> </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-12" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>How much does it cost to synthesize my oligo?</div> </a> </div> <div id="QA-12" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> Azenta offers several options for synthesis and cost depends on the synthesis type, length, scales, modifications, and purifications required. Please contact <a href="mailto:dnaseq@azenta.com">dnaseq@azenta.com</a> or +1-877-436-3949 ext. 2 with pricing inquiries or reach out directly to your Sales Representative. </div> </div> </div> <div class="NoBorder panel panel-default"> <div class="panel-heading SingleBorder" style="text-align:left;"> <a class="accordion-toggle" data-toggle="collapse" data-parent="#OLIGO-SYNTHESIS-FAQs" href="#QA-14" style="color:gray;text-align:left;"> <div class="QA col-sm-1">Q:</div> <div>Do you synthesize RNA?</div> </a> </div> <div id="QA-14" class=" panel-collapse collapse NoBorder"> <div class="panel-body NoBorder"> <div class="QA col-sm-1">A:</div> Yes, oligos containing RNA, LNA, 2-O-Me-RNA and other modified RNA nucleotides are available through our <strong>Custom Synthesis</strong> Service. Please submit an inquiry online through your Azenta account. </div> </div> </div> </div> </div> </div><script language="javascript" type="text/javascript"> jQuery(document).ready(function ($) { $(".SingleIcon").find("img").addClass("img-responsive center-block"); }); </script> <div class="process-v1 icon-nav Component-BackGround-Default margin-top-0 margin-bottom-30 padding-top-10 padding-bottom-10"> <div class="container"> <div class="headline-center"> <br> <br> <h1>Azenta Service FAQs</h1> <!--ul class="list-inline"> <li> <h3><a class="blue-text" href="/Public/Resources/FAQs/FAQs-DNA-Sequencing">Sanger Sequencing</a> </h3> </li> | <li> <h3><a class="blue-text" href="/Public/Resources/FAQs/FAQs-Gene-Synthesis">Gene Synthesis</a> </h3> </li> | <li> <h3><a class="blue-text" href="/Public/Resources/FAQs/FAQs-Next-Generation-Sequencing">Next Generation Sequencing</a> </h3> </li> | <li> <h3><a class="blue-text" href="/Public/Resources/FAQs/FAQs-Molecular-Genetics">Molecular Genetics</a> </h3> </li></ul--> <p></p> </div> <ul class="list-unstyled row row-centered"> <li class='col-md-3 col-sm-6 col-centered'> <a href='/Public/Resources/FAQs/FAQs-DNA-Sequencing' target=''> <div class='SingleIcon headline-center Component-BackGround-Default margin-top-0 margin-bottom-30 padding-top-10 padding-bottom-10'> <div class="row"> <img src="/-/media/Images/Home/icons/Purple-Icons/sanger-overview-110x210_Purple.ashx?h=110&la=en&w=210&hash=6A2D1890F8DD7B9B4EA2DA7B1AC514AC39C28B05" alt="Building" width="210" height="110" /> </div> <div class="row"> <h3>Sanger Sequencing</h3> </div> <div class="row"> </div> </div> </a> </li> <!--target=""--> <li class='col-md-3 col-sm-6 col-centered'> <a href='/Public/Resources/FAQs/FAQs-Gene-Synthesis' target=''> <div class='SingleIcon headline-center Component-BackGround-Default margin-top-0 margin-bottom-30 padding-top-10 padding-bottom-10'> <div class="row"> <img 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