Tutorials

Short step-by-step guides to get the most out of Visual Oligo. Start with Oligo Properties and Salt Adjusted Tm, then use the 3D viewer for DNA/RNA structures and Batch Analysis for multiple sequences.

• Oligo Properties (MW/Tm/GC)

  Enter a DNA or RNA sequence (5′→3′), or fetch by GenBank/RefSeq accession. Get length, molecular weight, GC%, Tm, and ε260. Download a PDF report. Use the primer pair section for forward/reverse Tm and suggested annealing temperature. For salt-adjusted Tm and molarity use Salt Adjusted Tm with MW from this tool.

• Salt Adjusted Tm (Molarity & Dose)

  Convert between mass (mg) and amount (nmol, μmol); compute stock concentration and dilution volumes. Enter molecular weight (from Oligo Properties or manually). Use for oligo resuspension, primer dilutions, and salt-adjusted Tm when the tool supports it.

• DNA/RNA 3D Structure

  Load an oligonucleotide or nucleic acid PDB (e.g. from RCSB). View in 3D, then export coordinates (PDB) or a screenshot (PNG) from the viewer sidebar. See Export formats for FASTA, PDB, PNG, PDF.

• Double Helix Builder

  Multi-frame or double-helix preview. Load a preset or your own PDB IDs to see trajectory or conformation playback. Export PNG as needed. For a single structure use DNA/RNA 3D Structure or PDB Upload.

• PDB Upload

  Upload your own DNA/RNA or oligonucleotide PDB file. View and export the structure as PDB or PNG. Use when you have a local structure from modeling or a collaborator.

• Batch Analysis Export

  Export multiple oligo analyses as a table (CSV) or a ZIP of PDF reports. Use Batch Analysis when available to enter multiple sequences and download results. See Batch Analysis Export for how to run batch export.

Getting Started · Melting Temperature Calculation · Export formats · Batch Analysis Export · FAQ