However, if two bases aren't complementary, they won't fit together. Instead, they'll repel each other, just like the identical poles of two magnets will repel each other. An A won't pair with a C, and a T won't pair with a G. So if there's even a single base that's not complementary to its partner, it could keep a single strand from sticking to another single strand.
http://www.affymetrix.com/corporate/media/genechip_essentials/dna_review/A_good_match_sticks__a_bad_match_doesn_t.affx
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