PCR and qPCR
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Increase the Tm of short, AT-rich primers and probes

Super T®—a duplex stabilizing, modified dT base

Quick facts:

Availability: DNA and RNA

Location: 5', internal, and 3'

Scales: 100 nmol to large scale

Purification: Standard desalt or HPLC

IDT Ordering Symbol: /5Super-dT/, /iSuper-dT/, /3Super-dT/

Super T® (5-hydroxybutynyl-2'-deoxyuridine; Figure 1) is a modified dT base that can be included in oligonucleotide primer and probe sequences to stabilize their hybridization. Super T base-pairing with dA during primer or probe hybridization provides an ~2°C increase in melting temperature (Tm) per Super T insertion. This Tm increase can be essential when working with short primers or probes that are AT rich.

The Super T modified base is extended normally by polymerases, including Taq polymerase.

How to order

To include Super T bases within your oligo, enter the IDT ordering symbol (/5Super-dT/, or /iSuper-dT/, or /3Super-dT/) in the desired location within your sequence. You can request Super T modified oligonucleotides with standard desalt or HPLC purification.

 Structure of 3′–3′ or 5′–5′ reversed linkages

Figure 1. Structure of 3′–3′ or 5′–5′ reversed linkages.

Further reading

Learn about other modifications that can be helpful in your oligonucleotide applications:

Oligonucleotide modifications: Choosing the right mod for your needs—Read these guidelines on selecting specific oligonucleotide modifications, and learn how they can help you in your research.

Modifications that block nuclease degradation—Find out about modifications that can be added to an oligo to limit nuclease degradation, for example, in experiments where the oligos will be used in cell culture or in vivo.

Need a non-standard modification?—IDT offers 89 modifications that are not listed in our online catalog. Here you can find out about a few of the more popular ones and learn how to order them. IDT will consider any modification you have in mind. Please make such inquiries to noncat@idtdna.com.

Author: Stephanie Youtsey is the Non-Catalog Coordinator in the Specialty and Manufacturing Services group at Integrated DNA Technologies.

© 2015 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see www.idtdna.com/trademarks.

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