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Oligonucleotide mass and fragments

DNA / RNA strand mass · 5' and 3' end groups · phosphodiester backbone fragments

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Oligonucleotide mass and fragments

Monomers are nucleoside monophosphates (dA 331.068 / dC 307.057 / dG 347.063 / dT 322.057 / dU 308.031), condensed into the strand; 5′/3′ ends can be hydroxyl or phosphate. Fragments are defined on the four cleavable phosphodiester-backbone bonds, so both sides of one bond add up to the parent strand.

Monomers are nucleoside monophosphates (dA 331.068 / dC 307.057 / dG 347.063 / dT 322.057 / dU 308.031), condensed into the strand; 5′/3′ ends can be hydroxyl or phosphate. Fragments are defined on the four cleavable phosphodiester-backbone bonds, so both sides of one bond add up to the parent strand.

Every calculation runs locally in your browser. Nothing you type is ever uploaded.

Open this calculator

Enter a DNA or RNA sequence (one letter: A/C/G/T/U), choose whether the 5' and 3' ends are hydroxyl or phosphate, and the tool builds the full strand formula by condensing nucleotide monophosphates with loss of water, reporting monoisotopic and average mass plus the m/z of every adduct. Single-stranded DNA, RNA and typical synthetic oligonucleotides can all be calculated directly.

The fragment table follows the four cleavable bonds of the phosphodiester backbone and matches the a/b/c/d and w/x/y/z nomenclature used in the literature; fragments from the two sides of a cleavage site sum to the parent strand, which makes the table self-consistent and handy for locating modifications in tandem MS. Every row lists monoisotopic and average m/z.

How to use it

  1. Type the sequence, such as ATCG or AUGC (U for RNA).
  2. Choose the nucleic acid type (DNA or RNA) and the 5' / 3' end groups (hydroxyl or phosphate).
  3. Set the ionisation and charge to read the strand mass and adduct m/z.
  4. Tick the fragment series you need and check that complementary fragments add back to the parent.

Frequently asked questions

What is the difference between DNA and RNA here?
RNA has an extra oxygen on the sugar ring (U instead of T, ribose instead of deoxyribose), so each nucleotide residue has a different mass. The tool uses the monophosphate monomer mass of the type you select, with end groups counted separately.
How much does a 5' phosphate add?
Exactly one HPO3, about 79.9663 Da. Synthetic oligonucleotides are usually hydroxyl at both ends, while enzymatic or native strands often carry a 5' phosphate - pick whichever matches your structure and the term is accounted for.
Is anything I type uploaded?
No. There is no back end: the algorithms, the NIST isotope data and every dictionary ship with the page, and all calculations run in your browser.
How accurate is the data?
Isotope masses and abundances come from a NIST snapshot (94 elements, 298 isotopes). Isotope distributions are exact polynomial convolutions and agree with mainstream simulators to several decimal places.
Is it free? Do I need an account?
It is completely free, with no usage limit and no sign-up or login.
Can I send a calculation to someone else?
Yes. Click Copy link and the input state is encoded into the URL hash, so opening that link restores exactly what you had.

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