Getting started with Visual Oligo

Visual Oligo provides research-grade tools for DNA/RNA oligonucleotides: molecular weight, Tm (melting temperature), GC%, salt-adjusted Tm, and 3D structure viewing (DNA/RNA 3D, Double Helix Builder). All in the browser; no installation required.

What we offer

Enter a DNA or RNA sequence (5′→3′) to get molecular weight, GC%, Tm, and ε260. Use Salt Adjusted Tm for molarity, stock concentration, and dilution (with MW from Oligo Properties). View DNA/RNA 3D structures and export PDB, PNG, or FASTA; batch analysis produces a table (CSV) or ZIP of PDF reports. Export options: Export formats, Batch Analysis Export.

Typical workflow

Single sequence: Go to Oligo Properties (MW/Tm/GC), enter DNA or RNA sequence (or fetch by GenBank/RefSeq). Get length, MW, GC%, Tm, ε260, and a PDF report. Use Salt Adjusted Tm for molarity and dilution.
Primer pairs: In Oligo Properties, use the primer pair section to enter forward and reverse sequences; get Tm difference and suggested annealing temperature.
3D view: Use DNA/RNA 3D Structure to load an oligonucleotide or nucleic acid PDB; use PDB Upload to load your own file. Export PDB or PNG from the viewer.
Double Helix Builder: Use Double Helix Builder for multi-frame or helix preview; export PNG.
Batch: Use Batch Analysis when available for multiple sequences; export table as CSV or ZIP of PDFs. See Batch Analysis Export for details.

Tools at a glance

Oligo Properties (MW/Tm/GC) — DNA or RNA sequence → length, MW, GC%, Tm, ε260, primer pair Tm; PDF report.
Salt Adjusted Tm — MW (from Oligo Properties), mass, volume → molarity, dilution; salt-adjusted Tm when applicable.
DNA/RNA 3D Structure — Load oligonucleotide or nucleic acid PDB; view, export PDB/PNG.
Double Helix Builder — Multi-frame or helix preview; export PNG.
PDB Upload — Upload DNA/RNA or oligo PDB; view and export.
Batch Analysis — Multiple sequences → table + CSV or ZIP of PDFs when available.

Export: Export, Export formats, Batch Analysis Export.

Docs and reference

Melting Temperature Calculation — Tm methods, salt adjustment, GC content.
Data sources — GenBank, IUPAC, RNAcentral, PDB.
Tutorials — Step-by-step for Oligo Properties, Salt Adjusted Tm, 3D viewer, Batch Export.
API — Programmatic access.