Isocaudomers are pairs of restriction enzyme

Restriction enzyme

A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...

s that have slightly different recognition sequences but upon cleavage generate identical termini. For example the enzymes Mbo I and BamH I are isocaudomers:

Mbo I
N*GATC N
N CTAG*N
BamH I
G*GATC C
C CTAG*G

N represents any of the four nucleotide

Nucleotide

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

s. Independently of which nucleotide is present when cleaving with MboI, after cleavage with either enzyme, all termini have the central tetranucleotide - GATC. This allows fragments generated with one enzyme to anneal with fragments generated with the other enzyme. This can be used for elimination of restriction sites from the resulting DNA fragment. For example:

Not I
GC*GGCC GC
CG CCGG*CG
Bsp120 I
G*GGCC C
C CCGG*G

In the above example, both enzymes produce tetranucleotides CCGG which can anneal to one another. However, resulting DNA sequence will be:
GCGGCCC
GCCCGGG
where the nucleotides shown in italic originate from NotI-cut site, and those in bold from Bsp120I-cut one. Note that the resulting sequence is not recognised by either of the two enzymes.

Other examples of isocaudomers include:

NcoI/PagI/PscI/NdeI

XbaI/NheI