Methods and kits for highly multiplex single primer extension

A method for performing a multiplex single primer extension reaction, comprising:

• (a) extending a plurality of different primers in a single primer extension reaction using a plurality of different double-stranded or partially double-stranded target nucleic acids as templates in a reaction mixture that comprises (1) a MutS protein and (2) Mg2+ at a minimum concentration of about 6 mM to generate extension products, wherein
• the plurality of different primers differs from each other,
• the plurality of different primers anneals to only one strand of the different double-stranded or partially double-stranded target nucleic acids, and
• the reaction mixture does not comprise a primer that anneals to the other strand of the different double-stranded or partially double-stranded target nucleic acids to exponentially amplify one or more of the different double-stranded or partially double-stranded target nucleic acids or a portion thereof except where most or all of the double-stranded or partially double-stranded target nucleic acids comprise a common sequence at least 10 nucleotides in length, a boosting primer comprising the common sequence or a portion thereof that is at least 10 nucleotides in length that anneals to a sequence complementary to the common sequence or a portion thereof in the other strand of the different double-stranded or partially double-stranded target nucleic acids is optionally present.