ZNA™ A Modified Oligonucleotide

ZNA: Zip Nucleic Acid

Sigma® proudly announces a worldwide licensing agreement with Polyplus-transfection to manufacture and commercialize Zip Nucleic Acids (ZNA); a new class of modified oligos for Molecular Biology and Molecular Diagnostic applications.

ZNA are novel synthetic modified oligonucleotides able to improve hybridization properties of nucleic acids. ZNA represents a new potent tool for numerous Molecular Biology applications.

Used as primers or probes particularly, ZNA™ improves PCR assays.

ZNA properties:

  • High affinity oligonucleotides
  • Adjustable and predictable melting temperature (Tm)
  • Fast binding to target sequence
  • Efficient as PCR primers or probes
  • Improved RNA to cDNA conversion during Reverse Transcription
  • Easy to design

ZNA: Concept of a versatile molecule
High affinity and Tm modulation
ZNA applications
ZNA as potent tools for PCR and RT-PCR
Purchasing ZNA
References and Patents

ZNA: Concept of a versatile molecule

The concept to develop ZNA was to increase the affinity of oligonucleotides for their target by decreasing the electrostatic repulsions due to the polyanionic nature of nucleic acids. This was achieved by conjugating spermine derivatives as cationic moieties (Z units) to an oligonucleotide.

The ZNA synthesis is carried out using an oligonucleotide synthesizer following the standard phosphoramidite chemistry. The automated synthesis of ZNA allows any modifications such as dyes and quenchers to be included.

ZNA molecules are versatile as the number of Z units can be chosen and placed anywhere within the oligonucleotide: in 5', 3' or in the middle. By selecting the number of cationic units, the global charge of the ZNA molecule can be modulated.

High affinity and Tm modulation

The melting temperature (Tm) of ZNA increases significantly and linearly with the number of cationic units grafted on the oligonucleotide, providing a convenient means for fine tuning hybridization temperatures.

Higher Affinity, Improved Binding and Faster Kinetics
ZNA exhibit an exceptional high affinity for their nucleic acid target mainly because they accelerate hybridization by binding to its target with fast kinetics.

Adjustable and Predictable
The Tm increases linearly with the number of grafted Z units, independently of the base sequence of the oligonucleotide and of the conjugation site of the cationic Z units (3' or 5'). The Tm increase per Z unit is only dependent on the length of the oligonucleotide. The Tm of the ZNA is then easily predictable, using a simple mathematical relation depending on the intrinsic DNA oligonucleotide Tm, on the length N of the oligonucleotide and on the number of Z cationic units (Noir et al., JACS 2008).
Tm (ZNA) = Tm (DNA) + 36z/(N-3.2)

Easy to Design
The required Tm is easily achieved by conjugating the appropriate number of spermines at either side of the oligonucleotide. The oligonucleotide sequence and the location of the cationic units do not affect the Tm increase provided by the spermine modification.

ZNA are Specific
ZNA display strict recognition selectivity. Similarly to standard oligonucleotides, ZNA specificity rely on optimized conditions including salt concentration, annealing temperature, and target and ZNA concentrations. Due to the higher affinity of ZNA, these conditions may differ from those optimized for standard


ZNA applications

ZNA performance have been successfully tested in PCR and RT-PCR as primers and probes (see below).

With their outstanding affinity and their high sensitivity, ZNA have a wide potential in Nucleic Acid-based technologies such as:

  • PCR / RT-PCR
  • Capture probes
  • Northern Blot / Dot Blot
  • Microarrays
  • In Situ Hybridization (ISH)

ZNA as potent tools for PCR and RT-PCR

ZNA primers and PCR probes show an exceptional high affinity for their targets.


ZNA primers provide flexibility for PCR assays:

  • Great performance at high annealing temperatures
  • Effective at very low concentrations
  • Robust amplification in AT-rich regions (see graph)
  • Efficient under short cycling conditions

ZNA primers in RT-PCR:

  • Improved RNA to cDNA conversion (see graph)
  • More accurate quantification of low-abundant transcripts

ZNA dual-labeled probes improve 5' nuclease assay sensitivity:

  • Facilitated design of 5’ nuclease assays
  • Efficient short probes and improved long probes
  • Earlier Cq values
  • High hybridization-triggered fluorescence


ZNA primer applications:
ZNA probe applications:
  • Fast PCR
  • Multiplex
  • AT-rich regions
  • High-throughput PCR
  • Reverse transcription
  • miRNA detection
  • SNP detection
  • AT-rich sequences

Purchasing ZNA

Custom ZNA oligonucleotides are now available for ordering.
Please contact dnaoligos@sial.com to request pricing information.




  • Voirin, E. et al. (2007) Versatile synthesis of oligodeoxyribonucleotide-oligospermine conjugates. Nat. Protoc., 2, 1360-1367.
  • Noir, R. et al. (2008) Oligonucleotide-oligospermine conjugates (Zip Nucleic Acids): a convenient means of finely tuning hybridization temperatures. J. Am. Chem. Soc., 130, 13500-13505.
  • Moreau et al. Zip nucleic acids (ZNAs): new high affinity oligonucleotides as potent primers for PCR and reverse transcription. NAR 2009 (in press).



Intellectual Property

  • is the worldwide exclusive licensee of the patent "Cationic oligonucleotides, automated methods for preparing same and their uses" WO/2007/069092 A2 filed by the Centre Nationale de la Recherche Scientifique (CNRS) the December 15, 2005;
  • owns conjointly with the CNRS and the Université De Strasbourg the patent "Method for hybridizing nucleic acids" filed the 27 Dec 2007 (Publication EP2075342A1 – 1 July 2009).