The expected fraction of clonable genomic DNA (Q803070)

The authors give an estimate of the fraction of unclonable nucleotides in simple form for parameter ranges within practical regimes. The presented approach is of a combinatorial nature. The central idea is to describe the different patterns of the distribution of restriction sites with respect to an arbitrary nucleotide such that it is not clonable. It turns out that in some cases only four sites, two on each side of the nucleotide, are sufficient to characterize these distributions, and the authors express the fraction in closed form. In other cases where the four sites do not provide sufficient information, upper and lower bounds are obtained. The conducted study shows that the fraction of unclonable nucleotides depends mainly on the maximum clonable length \((L+r)\), and in a minor way on the minimum clonable length (L). The main conclusion of this paper is that for most practical purposes, a reasonably good estimate of the fraction (F) of clonable nucleotides is: \[ M=e^{-p(L+r)},\quad F=1-M(1+p(L+r))-(1/6)p^ 2L^ 2M(pL+3), \] here p is the frequency of occurrence of restriction enzyme restriction sites.