Issue 29, 2016
From the journal:

Analytical Methods

Cy5/BHQ dye–quencher pairs in fluorogenic qPCR probes: effects of charge and hydrophobicity†

Valentina M. Farzan,a   Ilya O. Aparin,c   Olga A. Veselova,a   Alexander T. Podkolzin,a   German A. Shipulin,a   Vladimir A. Korshuncd  and  Timofei S. Zatsepin*abe  

* Corresponding authors

a Central Research Institute of Epidemiology, Novogireevskaya 3a, 111123 Moscow, Russia

b Skolkovo Institute of Science and Technology, 4 Nobel Street, Innovation Center “Skolkovo”, 143026 Skolkovo, Russia
E-mail: t.zatsepin@skoltech.ru
Fax: +7-495-939-5411
Tel: +7-495-939-5411

c Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia

d Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia

e Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1-3, 119992 Moscow, Russia

Abstract

For the first time we used a CuAAC click reaction for the synthesis of cyanine labeled qPCR probes. We performed the comparison of dyes and quenchers (Cy5 vs. disulfo–Cy5 and BHQ2 vs. BHQ3) in several TaqMan probes with different stability of the secondary structure. Based on the studies of thermal quenching of dyes and the increase of fluorescence during probe melting and in the course of qPCR, we suggest that the disulfo–Cy5–BHQ2 pair is a preferable one for molecular beacons due to the highest increase of fluorescence during melting. As the Cy5–BHQ3 pair gave a better Cq and a maximal relative increase of fluorescence in qPCR in comparison to others we recommend this pair for Taqman style probe design.

Graphical abstract: Cy5/BHQ dye–quencher pairs in fluorogenic qPCR probes: effects of charge and hydrophobicity

About
Cited by
Related
Download options Please wait...

Supplementary files

Article information

DOI
https://doi.org/10.1039/C6AY01304J
Article type
Paper
Submitted
03 May 2016
Accepted
23 Jun 2016
First published
27 Jun 2016

Anal. Methods, 2016,8, 5826-5831

Permissions

Request permissions

Cy5/BHQ dye–quencher pairs in fluorogenic qPCR probes: effects of charge and hydrophobicity

V. M. Farzan, I. O. Aparin, O. A. Veselova, A. T. Podkolzin, G. A. Shipulin, V. A. Korshun and T. S. Zatsepin, Anal. Methods, 2016, 8, 5826 DOI: 10.1039/C6AY01304J

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements