protocol - circularizing DNA molecules?

I have been reading about next-generation sequencing technologies that can sequence long reads. Even though the origin of my question is sequencing technologies, the question I am asking is about the basics of DNA biochemistry.

One of the issues in manipulating DNA samples seems to be the ability to circularize long linear DNA molecules into circular DNA molecules. What are the technical challenges of circularising DNA molecules longer than 50Kbp?

Answer

For ligation of a linear molecule to occur, the two ends must come together at the active site of the DNA ligase. In a simple molecular cloning experiment the aim is usually to avoid recircularisation of a cut plasmid vector, and instead to get a new fragment of DNA inserted into the vector. However because the ends of the linearised circular plasmid are tethered together (by being ends of the same molecule) they are more likely to encounter each other than they are to encounter the end of an incoming fragment. This is usually overcome, in part, by increasing the relative concentration of the target fragment.

If you are aiming to recircularise a long fragment then the opposite effect will come into play: the ends of individual long molecules will be much more independent and so the end of another molecule will be likely to compete successfully for ligation. In theory this effect could be overcome by reducing the DNA concentration, but I assume that this is impractical for other reasons.