MW calculator›Single strand

Define the oligonucleotide

Start with the sequence, then refine only the chemistry your experiment needs. Everything recalculates in the result panel.

Sequencetype, paste, or use Quick Insert · 5′ → 3′

Strand mode
Calculate one oligonucleotide strand.
Awaiting sequence
0 nt

Enter DNA/RNA bases 5′→3′. Spaces are ignored; modified bases use prefixes such as mA or fG.

Strand Configurationbackbone, linkage, and end groups

BackboneSugar identity 2′-H · d
LinkageInternucleotide bond 9 bonds · +557.68 Da
End groups5′ and 3′ contribution
+0.00 Da

Advanced Modificationmodified sugars, custom bases, catalog

Sugar modifications2′-OMe · 2′-F · MOE · cEt
Custom monomersFormula-aware · 0 saved
Vendor catalog30 free · 267 with Pro
Melting temperature›nearest-neighbour, per-residue coverage

Melting temperature

For the strand entered in the Calculator. Every number names the published model behind it, and says so when your chemistry has none.
PCR buffer: K⁺, Mg²⁺ and dNTP only matter in a polymerase reaction
Concentration›Nanodrop → molarity

Concentration & molarity

Use the current strand’s molecular weight automatically, or enter a known molecular weight for an external oligo.
Molecular weight
— g/mol
enter a sequence in the Calculator tab

This value replaces the linked sequence MW for the ng/µL and dilution calculations. A₂₆₀ is unavailable because that path needs a sequence-derived extinction coefficient.

Stock concentration · Nanodropε₂₆₀ 101,200 M⁻¹cm⁻¹

ng/µL
cm
Stock concentration
0
Total amount —
Total mass —

Dilute the stock · C₁V₁ = C₂V₂using the stock above

Stock used for the dilution
— stock
measured from the reading above

Use this when you already know the stock: a vendor tube with the concentration printed on it, or an aliquot you made earlier. It replaces the measured stock in the dilution recipe only. Section 1 keeps reporting whatever the reading above gives. With a stock you type in, the dilution needs no molecular weight and no sequence.

Add stock
—
Add water / buffer
—
Mass spec›ESI m/z ladder

Mass spec

Exact mass, elemental formula, and the ESI m/z ladder for the current strand.
Average mass
3,027.04g/mol
Monoisotopic mass
3,025.55Da
C₉₈H₁₂₄N₃₇O₅₈P₉net charge −910 nt · 9 PO
ESI− m/z ladder on the average basis (selected above); the result panel's ladder follows this toggle.
charge[M−zH]z− m/z+Na⁺+K⁺
1−3026.033048.013063.99
2−1512.511523.501531.49
3−1008.011015.341020.66
4−755.75761.25765.24
5−604.40608.80611.99
Rows marked working range land between 500 and 2000 m/z, which is what most ESI instruments are set to collect. Oligos ionise in negative mode, meaning they lose protons from the backbone rather than gain them. Which peak comes out tallest depends on your instrument and how it is tuned.
Vendor catalog›Monomer library

Vendor catalog

Browse tabulated phosphoramidite monomers. Insert drops a code into the sequence at the cursor; + Library promotes it to a permanent keypad key.
Free: 30 unique amidites · 45 vendor listings. Oligo Calculator Pro adds the full 267 unique · 351 listings.
⌕

30 free amidites

Filters and catalog help

Insert places the code at the cursor in your 5 prime to 3 prime sequence. + Library keeps it under More monomers.

↳ Insert places the code at the cursor in your 5′→3′ sequence on the Calculator tab. + Library makes it a permanent entry under More monomers.

2′-O-Methyl-A
mAChemGenes343.27 g/mol2′-sugar✓ verified
2′-Fluoro-C
fCChemGenes305.20 g/mol2′-sugar✓ verified
5-Methyl-dC
5MeCGlen Research303.25 g/molModified base✓ verified
LNA-G (locked)
+GQiagen344.24 g/molBridged 2′-sugar✓ verified
6-FAM (5′ fluorescein)
FAMGlen Research537.46 g/molLabel · dyeAverage mass available; monoisotopic mass unavailable
Library›Saved strands

Saved strands

Reopen, copy, or export a strand you saved. Signed in, your account holds the copy that travels between devices and this browser keeps an offline mirror; signed out, strands live in this browser only.
⌕
SelectSequenceActions
ATCGATCGAT demoATCGATCGATDNA · 10 nt3,027.04Jul 22
siRNA guide (2′-OMe/2′-F)
showhidemUfAmGfCmAfCmGfUmAfCmUfGmAfC
RNA · 14 nt4,713.02Jul 21
T7 promoter fwdTAATACGACTCACTATAGDNA · 18 nt5,560.63Jul 20

Select rows to export just those, or export all as CSV. Delete and Clear all ask for confirmation before removing anything.

Account›Lab

Lab

A lab is one shared library. Everyone in it sees the same strands and monomers, and everyone keeps their own work if the lab is ever closed.

Loading your lab…

Plans›Your account

Plans & account

Guest
The calculator is free and always will be. An account is what makes it yours: your strands, your monomers, on every device you use.
Guest
Not signed in. This browser only
Saved strands0 / 10
Kept in this browser only
Photo scans0 / 0
Needs a free account
EmailCodeDone

Create your free account

No password to invent or forget. We email you a 6-digit code, and that is the whole thing. The same box signs you in if you already have an account.

Codes only. There is no link to click. If a code is refused, ask for a new one. The newest email is the one that works.

You're signed in. Your account is on the Free plan: 50 strands and 10 scans to try. Your library syncs to this account, and this browser keeps an offline mirror of it.
Signed in
Your account · library syncing across your devices
The sign-in service handles sending the email, expiring the code and rate limits. We store your email and your strands. Nothing else.

Plans

Free
$0
Your library, on every device
  • 50 saved strands, synced to your account
  • 10 photo scans to try
  • Voice entry, unlimited
  • 30 verified amidites · 45 vendor listings
  • Install as an app · works offline
Most researchers
Pro
$9/month
For the bench you're at every week
  • Unlimited saved strands. A notebook that never fills
  • 20 photo scans a month
  • All 267 verified amidites · 351 vendor listings
  • Folders, tags, notes, batch export
  • Everything in Free
Lab
$6/seat/month
One library your whole lab writes to
  • Everything in Pro, for every member
  • A shared lab library for strands and custom monomers
  • From 3 seats, no upper limit · add more any time
  • 20 scans per seat, pooled across the lab
  • Roles, so a rotating student can't clear the library
Out of scans before the month is up?
A pack of 50 photo scans is $5, bought once. Not a subscription. The credits never expire, and your monthly scans still reset on their own.

Pooled scans are deliberate. A lab of five gets 100 scans a month from one pool, so the person running a screen is not rationed by the person who scanned nothing that week.

You never lose a strand by downgrading. A quota only stops new saves. Everything already in your library stays readable, exportable and editable on any plan, forever.

Academic labs get 40% off. Ask for a code. That is what the box above is for.

How lab plans work

The question everyone asks first: if my PI buys a lab plan, what happens to my account?

1Your PI gives you access by naming your email address. They add the exact address to the lab roster. There is no joining by university domain, because one university domain covers tens of thousands of people, not your lab. Naming one address is a deliberate act, which is the point.
2You open Oligo Calculator and sign in with that address. Same email, same 6-digit code, same box. The lab seat attaches itself the first time you sign in. We email you when your PI adds you, but the seat works whether or not that email arrives, so there is nothing to wait for and nothing to lose in a spam folder. There is no separate lab login and no lab URL to remember.
3You keep your own account. Joining a lab adds a shared library. It does not take over your personal one. Your own strands stay yours, including if you leave the lab.
4The lab pays, not you. If your lab covers you, we say so and grey out the Pro button instead of quietly taking a second payment.
What you get
Free
Pro
Lab
Calculator · Mass Spec · Concentrationevery mode, every modification
Full
Full
Full
Saved strands
50
Unlimited
Unlimited
Photo scanread a sequence off a label or a page
10 to tryone time
20per month
20 / seatpooled
Voice entry
Unlimited
Unlimited
Unlimited
Vendor catalogverified amidites
3045 listings
267351 listings
267351 listings
Library managementfolders · tags · notes · batch
—
Included
Included
Shared lab librarymembers · roles · custom monomers
—
—
Every seat
Install as app · offline
Yes
Yes
Yes
Price
$0
$9/mo
$6/seat/mo
Your library and the full catalog are Supabase-backed behind account auth, so an account really does unlock them. Nothing here is a flag we set in the browser. Billing isn't open yet. Until it is, Pro is granted by access code; the box in your account is where you enter one.
Oligo Calculator
Built and run by Yu-Sheng Chen, a PhD candidate in RNA chemistry in New York, out of pocket. The site is independent: not affiliated with, funded by or endorsed by any university. No analytics, no trackers. Check every mass before you pipette.