Changing the direction of backbone connections

HELM is a directional notation. For example, in RNA sequences the start of the chain is the 5’ end of the polymer and the end is the 3’ end.




This is encoded by the definition of the backbone connection.  R1 is connected to R2



However, there are times where the molecule you want to encode has a different backbone configuration, for example when the connection is reversed.


There are 2 options:

  1. Create a manually defined connection between different simple polymers.

  2. Define a new monomer with the R group numbers changed to reflect your desired connection points.


We recommend option 2.


If you use option 1, the original monomer, the HELM string would look like this:


It would take the user longer to construct using the available editing tools and is more prone to error. We don’t recommend this approach.


Creating a reversed connection using a new monomer

To reverse the connection in the example above, the user should define the monomer with the R1 and R2 groups swopped over. So, a reversed ribose monomer would look like this:


The guidelines define monomers where the capped structure is the same, but the connection points differ as different monomer, so both forms can be stored in a monomer library.

We also recommend that the monomer is named with the connection as a prefix to the monomer symbol so, in this case R becomes [35R] to show that it is now 3,5 connectivity.

Other common sugars would be numbered in a similar way:

               R              -> [35R]

               [dR]       -> [35dR]

               [mR]      -> [35mR]

               [fR]        -> [35fR]


So our original example becomes RNA1{[35R](C)P.[35R](A)}$$$$V2.0, the connection is reversed and the 5’ end is now on the right.


Canonicalization recommendations

If you reverse the whole of a simple polymer then you have a chain that could also be represented using standard monomers, just connected in the opposite order. For example:

RNA1{[35R](C)P.[35R](A)}$$$$V2.0          is the same as                    RNA1{R(A)P.R(C)}$$$$V2

We recommend that reversed monomers are only used where there is no alternative. In practice this will be when a sequence contains a combination of both forward and reverse sugars.