Welcome to the RNA/ssDNA pulling server !

This server performs quantitative
predictions of force-extension
curves of RNA or ssDNA
molecules. It takes the secondary
structure of the molecule fully
into account with the exception
of pseudoknots. The single-stranded
pieces of the molecule are modeled
as an elastic freely jointed chain.

Back to the Bundschuh group's server page or to the mirror at Terry Hwa's group.

Sequence information

Please enter a name for your sequence (mandatory):

Sequence (up to 1600 bases - if you need more, please contact us at rnapuller@bioserv.mps.ohio-state.edu):

You may input a sequence of the bases 'g', 'c', 'a', 't', and 'u' (upper or lower case) and the '@' character. The '@' character stands for a base which cannot interact with any other base. All other characters including spaces and line breaks are ignored.
Be aware that any sequence beyond 200 bases will take a noticable amount of time and may lead to a time-out on a busy day.

Do you want to pull on RNA or ssDNA ?

Your email address:

Parameter setting

You can tune different modelling parameters. Please keep them at their default values if you are not sure about what you are doing.

Environmental parameters

Temperature: oC
Concentration Na+: 1000 mM
Concentration Mg++: 0 mM

Physical properties of the single-stranded molecule

Base to base distance: nm
Persistence length: nm
Elasticity: nm

Ensemble definitions

structure ensemble or minimum free energy at one extension ?

all extensions or optimal extension only ?

If you want to know more about how the software behind this server works, please read the article

Ulrich Gerland, Ralf Bundschuh, and Terence Hwa, Force-induced denaturation of RNA, Biophys. J. 81 (2001), 1324-1332.

The secondary-structure prediction part of this software is an extension of the Vienna package described in

I.L. Hofacker, W. Fontana, P.F. Stadler, S.Bonhoeffer, M. Tacker, and P. Schuster, Fast folding and comparison of RNA secondary structures, Monatshefte f. Chemie 125 (1994) 167-188.

For questions and/or comments please send an email to rnapuller@bioserv.mps.ohio-state.edu.

Back to the Bundschuh group's server page.

8/22/00, Ralf Bundschuh, The Ohio State University