For both the present and the foreseeable future, the nucleotide sequence of DNA strands is determined by the electrophoresis of an ensemble (ladder) of single-stranded DNAs. Thus far, only polyacrylamide gels have had pores small enough to generate the sieving needed for DNA sequencing. The current procedures are, however, limited to the sequencing of 300-500 nucleotides per fractionation. To reduce both the number of samples prepared for electrophoresis and the difficulties in assembling partial sequences, particularly when the sequence is repetitive, lengthening the readable DNA sequencing ladder is needed. Increasing both the efficiency and reproducibility of DNA sequencing gels would also help to accomplish these goals. Thus, ideally, gels developed to lengthen readable DNA sequencing ladders would also be mass-producible. However, polyacrylamide gels are too storage-unstable for mass production. To lengthen DNA sequencing ladders, both pore size-gradient gels and alternative gel matrices are needed. For satisfying all of these needs, we have found that a newly investigated, gel-forming (non polyacrylamide) polymer has the following promising features: pores sufficiently small for DNA sequencing, probable storage stability, and formation of pore size-gradients by procedures adaptable to mass production. One of these procedures is our procedure for using an ion gradient to produce a pore size-gradient. By use of either this or an improved gel-forming compound, our first two specific aims are the following: (1) For the purposes of developing both robust pore size- gradient gels and improved uniform gels, both of which can be mass- produced for DNA sequencing, we will determine the sieving characteristics of gels as a function of conditions of gelation (ionic strength, pH, buffer type, temperature). We will use our previously- developed procedures to determine the gel's effective pore radius from the observed sieving of spheres. (2) By use of the data obtained under the first specific aim, we will develop procedures for producing both pore size-gradient gels and uniform gels that both lengthen electrophoretic DNA sequencing ladders and provide the advantages of mass-production. By use of field inversion, we will attempt to further improve the resolution of DNA sequencing ladders. Our third specific aim is a response to the needs of investigators who are developing capillary electrophoresis for the sequencing of DNA. (3) In response to these needs, we will explore the production of DNA sequencing ladders by electrophoresis in gels of compounds that have unusual gelling properties, including gelation when the temperature is raised. In addition to its use for the sequencing aspect of the human genome initiative, the data generated will contribute to understanding fundamental characteristics of gel-forming polymers.
