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Mobile DNA: Finding Treasure in Junk > 9. An experimental breakthrough

9. An experimental breakthrough

Beth Dombroski was an attractive, dark-haired young lady who had recently finished her Ph.D. in the Chemistry department at Johns Hopkins University with Tom Tullius. Her first paper had been a first-author paper in Science on a new method of DNA “foot-printing,” discovering where on a DNA molecule proteins interacted. She came from Reading, Pennsylvania, and had done her undergraduate degree at Shippensburg, a small, highly regarded, liberal arts university in Eastern Pennsylvania. She was eager to work on the biology of L1.

However, we still needed a hook to get into the problem. How would we separate a small group of L1 elements that contained the precursor to either the JH-27 or JH-28 element from the remaining very large number of irrelevant L1s? In other words, we needed a way to find the proverbial needle in a haystack. I knew of one reasonable possibility. Over the previous four years, the lab had used a technique devised by Bruce Wallace at City of Hope in which one could carry out a Southern blot using a very short, labeled probe (Itakura et al., 1984). Previously, Southern blot probes were 500 nucleotides or longer, but Wallace had shown that one could find in genomic DNA any exact match for a short probe of 18–20 nucleotides in length under the right conditions. These probes were called oligonucleotides, or oligomers, because they contained a relatively small number of nucleotides (but enough so that they would hybridize specifically). Moreover, they could be synthesized for any desired nucleotide sequence in special core labs. From 1983 to 1987, we had perfected Wallace’s technique of hybridizing an oligonucleotide probe to DNA fragments in a dried agarose gel. By this time, we knew the conditions that would allow hybridization of a 20-nucleotide oligomer to only its exact match in genomic DNA. If the match were 19 nucleotides out of 20, no hybridization signal would result.


  

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