I'm writing my master's thesis proposal, and I need to improve the solution-behavior of some truncated protein domains which have previously shown poor solubility when expressed in E. coli.
To prevent this unwanted aggregation, one experiment I will perform will be to alter the domain boundaries. I will create gene constructs where each clone will have an A domain of a certain length and domain border (see below).
My question: Is Gateway cloning better than restriction/ligase methods for this? If i use restriction/ligase methods to construct vectors for transformation, then my choice for domain boundaries will be determined by restriction sites. Howevever, with a system like Gateway cloning, I can define boundary limits to bp resolution by simply desining an appropriate primer.
Is my reasoning here correct? I need to justify my choises for experimental design to researchers, so want to make sure I'm being efficient and logical.