title: Zip Nucleic Acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription.
abstract: 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.
authors.affiliation: Polyplus-transfection SA, Bioparc, Illkirch, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Moreau
authors.forename: Emilie
authors.initials: E
authors.lastname: Voirin
authors.forename: Clément
authors.initials: C
authors.lastname: Paris
authors.forename: Mitsuharu
authors.initials: M
authors.lastname: Kotera
authors.forename: Marc
authors.initials: M
authors.lastname: Nothisen
authors.forename: Jean-Serge
authors.initials: JS
authors.lastname: Rémy
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Behr
authors.forename: Patrick
authors.initials: P
authors.lastname: Erbacher
authors.forename: Nathalie
authors.initials: N
authors.lastname: Lenne-Samuel
mesh_terms: D020856:AT Rich Sequence; D017931:DNA Primers; D016133:Polymerase Chain Reaction / Q000592:standards; D048348:Reverse Transcription
chemical_list: D017931:DNA Primers
references.citation: Biotechnol Bioeng. 2005 Nov 5;92(3):346-55
references.pmid: 16170827
references.citation: Clin Chem. 2004 Mar;50(3):509-15
references.pmid: 14726469
references.citation: Biochemistry. 2008 May 13;47(19):5336-53
references.pmid: 18422348
references.citation: J Am Chem Soc. 2008 Oct 8;130(40):13500-5
references.pmid: 18781743
references.citation: J Clin Microbiol. 2005 Sep;43(9):4868-71
references.pmid: 16145162
references.citation: Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3814-8
references.pmid: 7731989
references.citation: Mol Cell Probes. 2003 Oct;17(5):253-9
references.pmid: 14580400
references.citation: Chembiochem. 2006 Aug;7(8):1173-6
references.pmid: 16874748
references.citation: Anal Biochem. 1997 Feb 15;245(2):154-60
references.pmid: 9056205
references.citation: Genes Dev. 2007 May 1;21(9):1025-30
references.pmid: 17437991
references.citation: J Biol Chem. 1995 Jun 16;270(24):14712-7
references.pmid: 7782335
references.citation: Clin Chem. 2002 Aug;48(8):1329-37
references.pmid: 12142391
references.citation: Mol Aspects Med. 2006 Apr-Jun;27(2-3):95-125
references.pmid: 16460794
references.citation: Biochemistry. 2004 May 11;43(18):5388-405
references.pmid: 15122905
references.citation: Nucleic Acids Res. 2005 Nov 27;33(21):e182
references.pmid: 16314296
references.citation: Clin Chem. 2009 Apr;55(4):611-22
references.pmid: 19246619
references.citation: Biochim Biophys Acta. 2000 Nov 15;1494(1-2):23-7
references.pmid: 11072065
references.citation: Clin Biochem. 2004 Oct;37(10):930-2
references.pmid: 15369726
references.citation: Nucleic Acids Res. 2000 Jan 15;28(2):655-61
references.pmid: 10606668
references.citation: BMC Mol Biol. 2007 Oct 22;8:93
references.pmid: 17953766
references.citation: Nat Protoc. 2006;1(3):1559-82
references.pmid: 17406449
references.citation: Nucleic Acids Res. 1997 Jul 1;25(13):2657-60
references.pmid: 9185578
references.citation: Nucleic Acids Symp Ser (Oxf). 2008;(52):417-8
references.pmid: 18776431
references.citation: J Mol Endocrinol. 2005 Jun;34(3):597-601
references.pmid: 15956331
references.citation: Mol Biotechnol. 2004 Feb;26(2):133-46
references.pmid: 14764939
references.citation: Nucleic Acids Res. 2006;34(20):e142
references.pmid: 17071964
references.citation: BMC Res Notes. 2008 Aug 28;1:70
references.pmid: 18755023
references.citation: Biotechniques. 2002 Apr;32(4):768, 770, 772, 754-5
references.pmid: 11962598
references.citation: Biochem J. 2001 Mar 15;354(Pt 3):481-4
references.pmid: 11237851
references.citation: J Gen Virol. 1995 Apr;76 ( Pt 4):1057-62
references.pmid: 9049358
references.citation: J Clin Microbiol. 2001 Feb;39(2):485-93
references.pmid: 11158094
references.citation: Nat Protoc. 2007;2(6):1360-7
references.pmid: 17545974
references.citation: Biochemistry. 1991 Apr 30;30(17):4357-61
references.pmid: 2021627
references.citation: J Biomol Tech. 2004 Sep;15(3):155-66
references.pmid: 15331581
references.citation: Int J Mol Med. 2004 Apr;13(4):521-5
references.pmid: 15010851