DNA minor groove width for individual nucleotides?

Question

[whelp]

Hi,

I am currently looking into some DNA structural features. With tools such as DNAshape (http://rohslab.cmb.usc.edu/DNAshape/) it is possible to predict multiple measurements including the minor groove width (in ångström) for every nucleotide of a DNA sequence.

I am a little confused about how you can get a measurement for every single nucleotide. I thought a nucleotide is either located in a minor groove or not. What is the reference point for this ångström length measurement for an individual nucleotide?

Answer 1

[Kevin Blighe]

Each base pair can certainly can have a minor groove width (MGW), i.e., when one looks at either the template or coding strand at each base-pair along the DNA double helix. In the methods for that manuscript, they state:

For each MC prediction, the structural features at single-nucleotide resolution were analysed with Curves (20). We used a modified definition for assigning MGW measurements to a bp, in which the MGW definition is independent of the usage of strand 1 or 2 of the DNA duplex as the leading strand. Specifically, the MGW at a given bp was calculated by averaging groove width measurements over three levels [1, 0, +1] surrounding the plane of a given bp, with levels 0 and +1 representing the first two levels calculated by Curves (20) for a nucleotide, and 1 being the last level of the preceding nucleotide. This definition includes 50 and 30 inter-bp values and defines MGW as a direction-independent measure.

[source: http://rohslab.cmb.usc.edu/Papers/2013_NAR_DNAshape.pdf]

I've put in bold the important part. So, for the MGW determination, they just look along the DNA double helix and make the calculation independent of the strand, instead looking at the 'plane' surrounding each position.

Kevin