What is the meaning of the "d(...)2" notation when writing a DNA sequence?
Assuming that you were referring to this specific usage of d(CGCTAGCG)2, the image provided for the crystal structure clearly shows that the structure refers to the fact that two strands of deoxy-ribonucleotide oligos were dimerised to each other. 

Had the same structure been formed by double-stranded RNA instead, the resultant dsRNA duplex helix would be referred to as r(CGCTAGCG)2