Nucleic Acids Research Advance Access originally published online on August 20, 2009
Nucleic Acids Research 2009 37(19):e130; doi:10.1093/nar/gkp661
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Nucleic Acids Research, 2009, Vol. 37, No. 19 e130
© The Author 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses?by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
Zip Nucleic Acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription
1Polyplus-transfection SA, Bioparc, Boulevard S. Brant, BP90018 and 2LCAMB, CNRS-UdS UMR7199, Laboratoire de Chimie Génétique, B.P.24, 67401 Illkirch, France
*To whom correspondence should be addressed. Tel: +33 3 90406180; Fax: +33 3 90406181; Email: nlenne{at}polyplus-transfection.com
Received June 18, 2009. Revised July 24, 2009. Accepted July 24, 2009.
Most nucleic acid-based technologies rely upon sequence recognition between an oligonucleotide and its nucleic acid target. With the aim of improving hybridization by decreasing electrostatic repulsions between the negatively charged strands, novel modified oligonucleotides named Zip nucleic acids (ZNAs) were recently developed. ZNAs are oligonucleotide–oligocation conjugates whose global charge is modulated by the number of cationic spermine moieties grafted on the oligonucleotide. It was demonstrated that the melting temperature of a hybridized ZNA is easily predictable and increases linearly with the length of the oligocation. Furthermore, ZNAs retain the ability to discriminate between a perfect match and a single base-pair-mismatched complementary sequence. Using quantitative PCR, we show here that ZNAs are specific and efficient primers displaying an outstanding affinity toward their genomic target. ZNAs are particularly efficient at low magnesium concentration, low primer concentrations and high annealing temperatures, allowing to improve the amplification in AT-rich sequences and potentially multiplex PCR applications. In reverse transcription experiments, ZNA gene-specific primers improve the yield of cDNA synthesis, thus increasing the accuracy of detection, especially for genes expressed at low levels. Our data suggest that ZNAs exhibit faster binding kinetics than standard and locked nucleic acid-containing primers, which could explain why their target recognition is better for rare targets.