sequences from linking clones (clones that contain the DNA from the ends of two 

 adjacent large fragments) will facilitate map construction. The advantages of this 

 protocol over existing ones is the speed of generating results, the precision of the 

 ordering, the simplicity of data analysis, and the fact that the mapping process generates 

 sequence data as well. 



In addition to the traditional means of accomplishing the above tasks, the researchers 

 are also investigating ways of using amplification via the polymerase chain reaction 

 (PCR) to obtain DNA sequences from the ends of large fragments and from linking 

 clones. Ultimately, there are plans to generate linking clones directly via PCR and 

 thereby avoid some of the pitfalls of traditional cloning methods that make completing a 

 map difficult. The PCR-based sequencing strategies are also attractive because they can 

 be readily automated or adapted to existing automated technologies such as DNA 

 sequencers. 



Direct Visualization of Chromosomes and DNA Fragments (S. Levene, M. Maestre, 

 M. Salmeron, and C. Bustamante) — Two other second-generation mapping protocols 

 are being investigated. First, hybridization of genes directly on chromosomes that are 

 visualized with confocal microscopy is used to develop physical maps of intemiediate 

 resolution. Second, further scanning tunneling microscope (STM) development would 

 produce STM and DNA handling techniques that would allow the nucleotide sequence 

 to be read directly from an isolated fragment of DNA. 



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