If you're going to restriction enzyme cut the 40bp sequence out and use that for further downstream applications, then you'll want to calculate the molar concentration based on that.  If you're going to use the entire 400bp sequence, then you'll use that instead.

Hi Jenny,

Thanks for your reply. I am unable to use restriction enzymes, therefore I'm going to have to stick to the 400bp amplified sequence. I wanted to know the Molar concentration of the 40bp target sequence specifically, rather than the 400bp region. Would I just have to use the molecular weight of the 40bp sequence and ignore the remaining 360 bp sequence?

Thanks again.

The answer to your question really depends on what you're going to use that sequence for.  There are online calculators like through New England Biolab that will tell you the ratio of vector to insert to add based on the length of the sequence.  There is also an average number for the weight of a base pair, which I don't remember off the top of my head, but I remember finding that online at one point.  I don't really see the point of knowing just the size of the 40bp sequence, though, if you can't remove it from the larger 400bp sequence.  Whatever you're going to do with that sequence is always going to be 400bp, regardless, unless you are to cut out your sequence.  You can always PCR in cut sites, you know, and then you could easily cut and paste your sequence from there.