Hot-start PCR is a technique that improves PCR performance by reducing nonspecific amplification during the initial setup stages of the PCR. This unit describes hot-start PCR protocols which utilize primers containing temperature-sensitive modifications. The introduction of 4-oxo-tetradecyl (OXT) phosphotriester groups onto the 3' end of the primer allows for primer-based hot-start PCR that is amenable for use in a number of PCR-based applications. The protocols described in this unit utilize OXT-modified primers in applications such as standard thermal cycling PCR, fast thermal cycling PCR, multiplex PCR, and one-step reverse-transcription PCR. This method is also advantageous for instances where improved PCR specificity is desired and a hot-start polymerase suitable for your application is not available.
Multiplex PCR is an advantageous technique used in PCR applications to amplify multiple targets in a single reaction. As useful as it is, this technique presents a new set of challenges that further complicates PCR setup. For example, reactions are more prone to off‐target amplifications such as mis‐priming and primer dimer due to the increased number of primer pairs. Furthermore, preferential amplification of certain targets leads to an unequal distribution of amplicon products, making quantification and detection of problematic targets extremely difficult. To improve upon the problems specific to multiplex PCR, we evaluated Hot Start modified primers which contain either one or two thermolabile 4‐oxo‐tetradecyl (OXT) modifications to prevent DNA polymerase extension at low‐stringent temperatures, and that are released after a Hot Start activation step. Herein, we find that the singly‐modified primers provide greater amplification efficiency, specificity, and yield in the multiplex amplification of DNA targets. In reverse transcriptase PCR (RT‐PCR), the doubly‐modified primers have been proven to be the optimal choice. The presence of two thermolabile protecting groups allows for an efficient one‐step RT‐PCR reaction that provides high specificity for multiple targets. TriLink's innovative technology represents a convenient tool for multiplex PCR amplification of DNA and RNA samples.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.