HOW IS IT THAT MICROSATELLITES AND RANDOM OLIGONUCLEOTIDES UNCOVER DNA FINGERPRINT PATTERNS

Minisatellites, microsatellites, and short random oligonucleotides all uncover highly polymorphic DNA fingerprint patterns in Southern analy sis of genomic DNA that has been digested with a restriction enzyme ha ving a 4-bp specificity. The polymorphic nature of the fragments is at tributed to tandem repeat number variation of embedded minisatellite s equences. This explains why DNA fingerprint fragments are uncovered by minisatellite probes, but does not explain how it is that they are al so uncovered by microsatellite and random oligonucleotide probes. To c larify this phenomenon, we sequenced a large bovine genomic BamHI rest riction fragment hybridizing to the Jeffreys 33.6 minisatellite probe and consisting of small and large Sau3A-resistant subfragments. The la rge Sau3A subfragment was found to have a complex architecture, consis ting of two different minisatellites, flanked and separated by stretch es of unique DNA. The three unique sequences were characterized by seq uence simplicity, that is, a higher than chance occurrence of tandem o r dispersed repetition of simple sequence motifs. This complex repetit ive structure explains the absence of Sau3A restriction sites in the l arge Sau3A subfragment, yet provides this subfragment with the ability to hybridize to a variety of probe sequences. It is proposed that a l arge class of interspersed tracts sharing this complex yet simplified sequence structure is found in the genome. Each such tract would have a broad ability to hybridize to a variety of probes, yet would exhibit a dearth of restriction sites. For each restriction enzyme having 4-b p specificity, a subclass of such tracts, completely lacking the corre sponding restriction sites, will be present. On digestion with the giv en restriction enzyme, each such tract would form a large fragment. Th e largest fragments would be those that contained one or more long min isatellite tracts. Some of these large fragments would be highly polym orphic by virtue of the included minisatellite sequences; by virtue of their complex structure, all would be capable of hybridizing to a wid e variety of probes, uncovering a DNA fingerprint pattern.