What is the future of electrophoresis in large‐scale genomic sequencing?

Abstract

Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.

Use of nanomaterials in capillary and microchip electrophoresis

“…As for the genomic sequencing, nanopores are utilized to sequence polynucleotides as they move through narrow channels under an applied electric field, this method promises high throughput [106,107]. Moreover, MCE utilizes the Sanger sequencing method for genome sequencing [108], thus, it is expected that the combination of both technologies will play an important part in genome sequencing in the future. In proteomics, enzyme-modified nanomaterials have been used for oncolumn digestion of proteins that are subjected to subsequent CE separation [91].…”

Electrophoretic migration of proteins in semidilute polymer solutions

“…Using different geometric models, in which simple objects represent sieving matrix and the moving molecule, various expressions have been derived [53]. For spherical molecules migrating in array of cylindrical fibers, the retardation coefficient is shown to be proportional to (R g 1 r) 2 where R g is the radius of gyration of denatured protein fragment and r is the radius of gel fibers. The wormlike chain model [54] predicts that the radius of gyration, R g , of a flexible molecule (such as DNA) is proportional to square root of molecular weight, M 1=2 w , of the migrating molecule.…”

“…Gel electrophoresis is the most commonly used method for separation of DNA and proteins of different electrophoretic mobilities. Chemical, biological, and pharmaceutical applications of electrophoresis were recently discussed in detail in a special issue of the Electrophoresis journal [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15]. In addition to developments in the field of conventional CE, rapid progress has also been made in developing microfabricated devices for high-throughput separation of DNA and proteins [15][16][17][18][19][20][21][22][23][24][25][26].…”

A molecular dynamics simulation study on trapping ions in a nanoscale Paul trap

“…Much research attention has been focused recently to the possibility of sequencing genome by measuring the base-type specific properties of each nucleotide as it migrates through a nanoscale pore (Chan, 2005;Fredlake et al, 2006;Healy, 2007;Kricka et al, 2005;Nakane et al, 2003;Burns, 2006, 2007;Ryan et al, 2007). However, it has been realized that repeatable measurements of the base specific signature of each nucleotide depends critically on the relative geometry of the bases to the pore during the DNA sequencing (Lagerqvist et al, 2007;Tabard-Cossa et al, 2007).…”