High Speed Automated DNA Sequencing in Ultrathin Slab Gels

Kostichka, Anthony J.; Marchbanks, Michael L.; Brumley, Robert L.; Drossman, Howard; Smith, Lloyd M.

doi:10.1038/nbt0192-78

Cited by 73 publications

(29 citation statements)

References 19 publications

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“…Closing (8)(9)(10) and reusable capillary gels (11,12) reduce the sequencing electrophoresis time to <1 hr and the detection limit to a few thousand fluorescent molecules per band (10-20 mol), the modular primers can be expected to decrease the time per walking cycle to 1 or 2 hr from the time of several days it now takes.…”

Section: Discussionmentioning

confidence: 99%

DNA sequencing: modular primers assembled from a library of hexamers or pentamers.

Kotler

Zevin-Sonkin

Sobolev

et al. 1993

Proc. Natl. Acad. Sci. U.S.A.

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Here we report a striking effect displayed by "modular primers," which consist of hexamer or pentamer oligonucleotide modules base-stacked to each other upon annealing to a DNA template. Such a combination of modules is found to prime DNA sequencing reactions uniquely, unlike either of the modules alone. We attribute this effect in part to the increase in the affinity ofan oligonucleotide for the template in the presence of an adjacent module. All possible pentamer (or hexamer) sequences total 1024 (or 4096) samples, a manageable size for a presynthesized library. This approach can replace the synthesis of primers, which is the current bottleneck in time and cost of the primer walking sequencing, and can allow full automation of the closed cycle of walking.

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Section: Discussionmentioning

confidence: 99%

DNA sequencing: modular primers assembled from a library of hexamers or pentamers.

Kotler

Zevin-Sonkin

Sobolev

et al. 1993

Proc. Natl. Acad. Sci. U.S.A.

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“…The 4200 has 64 lanes and can produce read lengths of 1000 bases from each end of the template with 99% accuracy or 60 bases in under 3 hr. (Kostichka et al 1992) was launched in early 2000. The system includes an eightchannel robot well loader with a minimum volume of 3 µL, so no manual loading is required.…”

Section: Slab-based Sequencersmentioning

confidence: 99%

Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends

Meldrum¹

2000

Genome Res.

116

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Automation for genomics has enabled a 43-fold increase in the total finished human genomic sequence in the world in the past four years. This is the second half of a two-part, noncomprehensive review that presents an overview of different types of automation equipment used in genome sequencing. The first part of the review, published in the previous issue, focused on automated procedures used to prepare DNA for sequencing or analysis. This second part of the review presents a look at available DNA sequencers and array technology and concludes with a look at future technologies. Alternate sequencing technologies including mass spectrometry, biochips, and single molecule analysis are included in this review.Sequencing data, essential for many of the medical breakthroughs of today and tomorrow, is currently accumulating at an exponential rate, largely because of advances in sequencing methods and laboratory automation. Instruments are available that can automate nearly every step in the large-scale sequencing process.The first article in this two-part review (Meldrum 2000) presented a description of automation designed for isolating DNA, cloning or amplifying DNA, preparing enzymatic sequencing reactions, and purifying DNA. Part one of the review also showed that the majority of genome centers use both in-house automation and commercial automation (Collins et al. 1998;Wendl et al. 1998;Mullikin and McMurragy 1999;Spurr et al. 1999; see http://www.genome.org for a supplementary table providing a snapshot view of automation used at a number of different genome centers).In this, the second part of the review, the focus is on automation after DNA preparation and sequencing reactions-on obtaining the sequence and its analysis. A discussion of future technologies for DNA sequencing projects is also included. (See the web sites referenced for photos or further details on the instruments presented.)

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“…However, gel electrophoresis is a time-consuming process that normally requires at least a few hours. Recently, capillary gel electrophoresis 5 and ultra-thin gel electrophoresis 6 have made significant progress in increasing sequencing speed. Nevertheless, speed is still limited by gel running time and time required for labeling.…”

mentioning

confidence: 99%

Matrix-assisted Laser Desorption/Ionization for Sequencing Single-stranded and Double-stranded DNA

Taranenko¹,

Chung²,

Zhu³

et al. 1997

Rapid Commun. Mass Spectrom.

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The DNA sequence of a single-stranded and double-stranded template was determined. The templates were sequenced using the chain termination method and cycle sequencing method and detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The sequencing products were analyzed successfully without the laborious and expensive methods for removal of the template. Direct sequencing of the double-stranded template was achieved with minimal post-reaction purifications, which could be extremely important for mutation analysis and clinical diagnosis. A systematic study of the mechanisms and kinetics of sequencing reactions was also performed. The details of this analysis and directions for future improvements of the quality of sequencing are presented.

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High Speed Automated DNA Sequencing in Ultrathin Slab Gels

Cited by 73 publications

References 19 publications

DNA sequencing: modular primers assembled from a library of hexamers or pentamers.

DNA sequencing: modular primers assembled from a library of hexamers or pentamers.

Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends

Matrix-assisted Laser Desorption/Ionization for Sequencing Single-stranded and Double-stranded DNA

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