The 3C (chromosome conformation capture) technology for studying chromatin 3D organization starts by a cross-linking step using formaldehyde to find segments of DNA interacting. In my understanding the cross-linking happens only between the DNA and proteins forming a DNA-protein-DNA complex. The "only" is from a DNA stand-point as of course protein-protein cross-links will also occur.
Can formaldehyde cross-link two double stranded DNA molecules? Is the 3C approach also capturing direct DNA-DNA interactions?
I looked at the literature, especially Dekker et al. description of the method, but couldn't find this information. Thanks.