Assign bases to minor and major groove

[KerstinRe]

Dear Xiang-Jun,

I have a question: how can I assign bases to be located in the minor or in the major groove based e.g. on the "analyze: Minor and major groove widths"?
Is it even possible with those values or do I need another approach?
I ask because it is e.g. not always possible/advisable to just assume that the minor and major groove "switch" every 5 bases.
Thanks in advance!

Best regards,
Kerstin

[xiangjun]

Hi Kerstin,

Thanks for posting on the 3DNA Forum!

If I understand your questions correctly, my answer would be: no, one cannot assign bases to minor or major groove. Assuming a double helix consisting of only Watson-Crick (WC) pairs, each base has both a minor and a major groove edge depending on your viewpoint. At the base pair level, each WC pair has two edges due to the asymmetric glycosidic linkage between the base and sugar moiety. Two grooves are formed when the pairs stack together forming a helix. Depending on the conformation of the helix, the two grooves can have different widths and depths. The most noticeable examples are the A- and B-forms.

Assigning a base to the minor or major groove makes sense only with reference to a helix (or a WC/wobble pair). The classic example is the A-minor motif where A is located in the minor-groove side of a WC pair.

THT,

Xiang-Jun