DNA structure with sequence-dependent structural characteristics

[deligkaris]

Dear all,

my understanding is that currently we can create with 3DNA, DNA structures with average parameters for dihedral angles, angles and parameters. Is it possible to create DNA structures with sequence-dependent characteristics, such as minor groove compression in PURINEpPYRIMIDINE steps, compression of major groove in PYRIMIDINEpPURINE steps etc?

Thank you,

Christos

[xiangjun]

Hi Christos,

To clarify, 3DNA's rebuild program can generate an 'arbitrary' DNA (or RNA) structure based on a set of base-pair (optional) and step (or helical) parameters. It is a mechanic process since the program does not check or care if the structure is realistic or not. It is mathematically rigorous because you can 'analyze' the generated structure to get  exactly the parameters you start with.

Now to your question -- yes, it is possible to "create DNA structures with sequence-dependent characteristics". As a practical example, see recipe #2 "Determination of DNA curvature associated with different roll distributions" in the 2008 3DNA Nature Protocols paper. As for building DNA structures with "minor groove compression in PURINEpPYRIMIDINE steps, compression of major groove in PYRIMIDINEpPURINE steps", it is up to you to derive the "correct" base sequence and base-pair parameters to feed into rebuild.

HTH,

Xiang-Jun