Table 17.1.

Comparison of methods for creating random double-strand breaks in acceptor DNA in order to create domain insertion libraries

	DNase I	S1 nuclease	Multiplex inverse PCR
Pros	More random than S1 nuclease Some tandem duplications produced	Easier library creation than DNase I Unlike DNase I, not prone to large deletions	Creates focused library The distribution of direct insertions, tandem duplications, and deletions is user-defined Easier library creation Allows for simultaneous creation of linker libraries at insertion site Shorter series of steps
Cons	Library construction is challenging Prone to large deletions Large fraction of library inserted outside gene or out of frame	May not be as random as DNase I Prone to insertions at sequences that produce stem-loop structures, such as inverted repeats May not produce tandem duplications at insertion site Large fraction of library inserted outside gene or out of frame	Requires large sets of primers and many PCR reactions Library is less diverse Creation of large tandem duplications problematic
References	Guntas et al. (2005, 2004), Guntas and Ostermeier (2004), and Wright et al. (2011)	Tullman et al. (2011) and Wright et al. (2011)	This work