Duplexr folds two DNA or RNA strands into their hybrid secondary structure — free, in your browser, with nothing to install.
Paste a primer and its target, an oligo probe and its amplicon, or any two sequences up to 300 nucleotides. Duplexr predicts how they hybridize, reports the thermodynamics, and draws the duplex as a 2-D structure you can pan, zoom, rotate and export.
The fold itself is delegated to the ViennaRNA Package (RNAcofold) — the same engine behind our desktop product OligoPAD — so the numbers are the ones you would get from the command line, without the command line.
At a glance
- Free to use — no licence, no installation, no account required
- DNA and RNA — five energy parameter sets, incl. DNA Mathews 1999 & 2004
- Up to 300 nt per strand, temperature 20 – 90 °C
- Four thermodynamic readouts from a single fold
- Interactive 2-D canvas with pan, zoom, rotate and base selection
- SVG and PNG export for reports and lab notebooks
- Runs everywhere — any modern browser, Windows, macOS, Linux
One fold, four numbers
Thermodynamics you can act on
Every fold returns the full energetic picture of the pair, not just a melting-point estimate — so you can tell a strong intended duplex from an accidental self-structure at a glance.
ΔGMFE
Minimum free energy
The single most stable structure the two strands can form.
ΔGens
Ensemble free energy
The partition function over all structures — how committed the pair really is.
ΔGbind
Binding energy
FAB − FA − FB — the part that is genuinely intermolecular.
( ) . ( )
Dot-bracket & 2-D plot
The structure itself, as notation and as a drawing you can export.
How it works
From two sequences to a picture in three steps
1Paste both strands
Type or paste strand A and strand B. Duplexr counts the bases, validates the alphabet and flags anything it cannot fold.
2Set the conditions
Choose the temperature and, if you need to, the energy parameter set, dangling-end treatment, G·U handling and loop constraints.
3Fold, inspect, export
Read the energies, explore the structure on the canvas, then save it as SVG or PNG for your report.
In the lab
What people use it for
- Primer and probe checks — does the oligo bind where it is supposed to, and only there?
- Assay design sanity checks — primer–primer and probe–target interactions before ordering
- Padlock and ligation probes — verify the arms hybridize as designed
- Aptamer and miRNA work — inspect predicted duplex geometry
- Teaching and publication figures — a clean, exportable structure drawing in seconds
Strand A, strand B and the inter-strand base pairs are colour-coded, so a mis-hybridization is visible before you read a single number.
Under the hood
Specification
| Folding engine | ViennaRNA Package, RNAcofold (heterodimer partition function) |
|---|---|
| Sequence length | 1–300 nucleotides per strand |
| Alphabet | DNA and RNA; T ↔ U is converted to match the chosen parameter set |
| Energy parameters | DNA Mathews 1999 (default), DNA Mathews 2004, RNA Turner 2004, RNA Turner 1999, RNA Andronescu 2007 |
| Temperature | 20 – 90 °C |
| Fold options | Dangling ends 0/1/2, forbid lonely pairs, forbid G·U pairs, forbid G·U closing pairs, minimum loop size |
| Layout algorithms | Simple radial and NAView |
| Export | SVG (vector) and PNG |
| Requirements | A current browser. Nothing to install, nothing to maintain. |
| Account | Optional. Guests get a watermark on the canvas and exports; signing in removes it. |
Where to go next
When a quick check is not enough
Credits. Folding is powered by the ViennaRNA Package (Hofacker lab, University of Vienna). Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011). ViennaRNA Package 2.0. Algorithms for Molecular Biology, 6:26.