ZNA primers and probes

Zip nucleic acids (ZNA®) are oligonucleotides conjugated with cationic spermine units. This asset decreases the electrostatic repulsion between single strand nucleic acids (i.e. between primer/ probe and target DNA during annealing). As a result, ZNA® primers and probes have higher affinity to their targets, compared to unmodified oligonucleotides.

Moreover, the global charge of a ZNA® oligonucleotide-oligocation can be modulated by specifying the number of cationic spermine moieties attached to the nucleic acid oligomer. The Tm of ZNA®increases linearly with the length of the oligocation. Therefore, it is possible to easily predict the melting temperature (Tm) of ZNA®-DNA or ZNA®-RNA hybrids.

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ZNA® advantages at a glance

... featuring

  • enhanced/accelerated target recognition
  • increased sensitivity
  • high specificity
  • increased Tm for short probes
  • improved quenching for long probes
  • increased flexibility in terms of
    • efficiency at low oligo concentration
    • efficiency at high annealing temperatures
    • Mg2+ concentration adjustment
    • design/sequence composition constraints
  • Probes for post PCR melting curve analysis
  • Enhanced primer/probe sensitivity and specificity through incorporation of base analoga (pdC, pdU)

... providing for

  • efficient mismatch/SNP/allelic discrimination
  • earlier Ct values
  • improved quantification accuracy of low abundancy transcripts
  • improved RNA to cDNA conversion
  • higher signal level
  • targeting highly conserved, specific (including A/T rich) sequences
  • universal cycling conditions due to 'Tm leveling' effects (stabilization of A/T rich duplexes), hence supporting multiplex assays
  • An excellent alternative to MGB and LNA

... hence qualifying for

a wide range of Nucleic Acid-based applications like

  • PCR / real-time PCR/RT-PCR
  • Microarrays/Capture probing
  • Northern Blot / Dot Blot
  • In Situ Hybridization (ISH)
  • Blocking of alleles (clamp PCR)
  • Next generation sequencing

What we offer

  • Primers as short as 10mers and dual labelled probes as short as 8mers, because the relative Tm increasing effect of ZNA (or other duplex stabilizing groups) is naturally higher on shorter oligonucleotides used as primers or probes.
  • The possibility to add ZNA®-building blocks, both at the 3’ and at the 5’-end of your DNA sequence.
  • Standard length range between 10 and 40 nucleotides for primers and probes. For longer sequences, please inquire.
  • For primers, 4 standard ZNA® building block modifications: ZNA-2, ZNA-3, ZNA-4, and ZNA-5!

    • ZNA-2 for oligos ≥ 8mers
    • ZNA-3 for oligos ≥ 12mers
    • ZNA-4 for oligos ≥ 16mers
    • ZNA-5 for oligos ≥ 20mers
  • For probes, 3 standard ZNA-Quencher (Q*ZNA-X) building block modifications for 3´labeling (For 5´ ZNA-Reporter labeling, please inquire!); Respective choice of 3´building blocks will be made automatically by metabion according to the following scheme:

    • 3' Q*ZNA-2 for probes ≥ 8mers
    • 3' Q*ZNA-3 for probes ≥ 14mers
    • 3' Q*ZNA-4 for probes ≥ 18mers
  • Additional modifications, like C-5 propynyl-dC (pdC) and C-5 propynyl-dU (pdU), which will further raise the Tm to ~2.8°C and ~1.7°C per substitution, respectively.
  • HPLC and documented Mass-Check QC included
  • 5´ZNA modified dual labeled probes, introducing 5´reporters like FAM, Fluo, JOE, ROX, TAMRA, etc (see table below)

With appropriate design, ZNA® probes can be used for high resolution post-PCR melting curve analysis (HRM). Please inquire at info@metabion.com and we will prepare a design for you!

All ZNA® oligos will be delivered dissolved in purified distilled water (pH 7-9), with a concentration of 100 µM (for special requests, please inquire)

Reporter-quencher combination

3' Quencher
  BHQ®-1 BHQ®-2 BBQ®-650 Eclipse® Dabcyl    
Abs range (nm) 480-580 550-650 550-750 390-625 380-550    
Abs max (nm) 535 579 650 522 453    
5' Reporter Possible combinations Abs (nm)* Em (nm)*
Fluo     450 500
6-FAM     495 520
TET     521 536
JOE     522 548
Yakima Yellow®     530 549
Hex 535 556
Cy3       546 563
ROX   576 601
Texas Red®     586 610
LC® Red 610     590 610
LC® Red 640       625 640
Cy5       646 662
Cy5.5       683 705
IRDye®700       685 705

*Please note that absorption and emission wavelengths are influenced by the solvent (pH, salt conditions, etc.), oligo sequence and other factors.


Order Forms

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Also available in our web order portal (WOP)

Useful Resources 

Noir, R. et al. (2008), J Am Chem Soc, 130, 13500-13505 download PDF
Voirin, E. et al. (2007), Nat Protoc, 2, 1360-1367 download PDF

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