An oligonucleotide hybridization approach to DNA sequencing

Khrapko, Konstantin; Lysov, Yu. P.; Khorlyn, A.A.; Shick, V.V.; Florentiev, V. L.; Mirzabekov, Andrei D.

doi:10.1016/0014-5793(89)81730-2

Cited by 228 publications

(97 citation statements)

References 4 publications

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“…From initial attempts to develop a method for largescale, low-cost sequencing of genomic DNA [108][109][110], the technology has diversified enormously and is now applied in nearly every area of nucleic acid analysis. Concomitantly, the kind of data produced in such studies is much different from earlier results in biology in so far as they are too complex to be analyzed and interpreted directly.…”

Section: Dna Microarraysmentioning

confidence: 99%

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

Sobek¹,

Bartscherer²,

Jacob³

et al. 2006

CCHTS

110

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Over the last years microarray technology has become one of the principal platform technologies for the highthroughput analysis of biological systems. Starting with the construction of first DNA microarrays in the 1990s, microarray technology has flourished in the last years and many different new formats have been developed. Peptide and protein microarrays are now applied for the elucidation of interaction partners, modification sites and enzyme substrates. Antibody microarrays are envisaged to be of high importance for the high-throughput determination of protein abundances in translational profiling approaches. First cell microarrays have been constructed to transform microarray technology from an in vitro technology to an in vivo functional analysis tool. All of these approaches share a common prerequisite: the solid support on which they are generated. The demands on this solid support are thereby as manifold as the applications themselves. This review is aimed to display the recent developments in surface chemistry and derivatization, and to summarize the latest developments in the different application areas of microarray technology.

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Section: Dna Microarraysmentioning

confidence: 99%

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

Sobek¹,

Bartscherer²,

Jacob³

et al. 2006

CCHTS

110

View full text Add to dashboard Cite

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“…The two main approaches for determining the sequences of DNA are shotgun sequencing and sequencing by hybridization (SBH) [5,8,11,13].…”

Section: Introductionmentioning

confidence: 99%

DNA sequencing by hybridization with additional information available

Formanowicz¹

2005

CMST

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Abstract:In classical DNA sequencing by hybridization it is assumed that the information obtained in the biochemical stage of the method is a set of the l-tuples composing the target sequence. It means that the information concerning the number of the repeated l-tuples is not available. Such an assumption was justified by the DNA chip technology constraints. However, nowadays some approximate information about l-tuple multiplicities can be obtained in the experiments, where DNA chips are used. It was a motivation for formulating combinatorial problems which arise when such additional information is taken into account. The goal of this paper is to formulate and classify these problems, what should establish a good starting point for further research concerning algorithmic methods solving DNA sequencing problems with multiplicity information. Moreover, the computational complexity of the new problems is determined, which in most cases is analogous to the complexity of their classical counterparts.

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“…Three DNA sequencing platforms are now being used to scan for mutations and polymorphisms. These include Sanger DNA sequencing [22] hybridizationbased sequencing [4,6,10,23,24] and Pyrosequencing [17,20]. Pyrosequencing is based on the detection of released pyrophosphate (PPi) during DNA synthesis.…”

Section: Introductionmentioning

confidence: 99%

Discovery of single nucleotide polymorphisms and mutations by Pyrosequencing

Ronaghi

Elahi

2002

Comp Funct Genom

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Comparative genomics, analyzing variation among individual genomes, is an area of intense investigation. DNA sequencing is usually employed to look for polymorphisms and mutations. Pyrosequencing, a real-time DNA sequencing method, is emerging as a popular platform for comparative genomics. Here we review the use of this technology for mutation scanning, polymorphism discovery and chemical haplotyping. We describe the methodology and accuracy of this technique and discuss how to reduce the cost for large-scale analysis. Copyright # 2002 John Wiley & Sons, Ltd.Keywords: SNP; Pyrosequencing; re-sequencing; bioluminescence; haplotyping; mutation detection; luciferase Determination of mutations and polymorphisms in a genome is one of the most important tasks in the studies of biological systems today. Three DNA sequencing platforms are now being used to scan for mutations and polymorphisms. These include Sanger DNA sequencing [22] hybridizationbased sequencing [4,6,10,23,24] and Pyrosequencing [17,20]. Pyrosequencing is based on the detection of released pyrophosphate (PPi) during DNA synthesis. In a cascade of enzymatic reactions, visible light proportional to the number of incorporated nucleotides is generated (Figure 1). The cascade starts with a nucleic acid polymerization reaction in which inorganic pyrophosphate (PPi) is released as a result of nucleotide incorporation by polymerase. The released PPi is subsequently converted to ATP by ATP sulfurylase which provides the energy to luciferase to oxidize luciferin and generate light. Since the added nucleotide is known, the sequence of the template can be determined (Figure 1). Pyrosequencing has the potential advantages of accuracy, flexibility, parallel processing and can be easily automated. Furthermore it dispenses with the need for labelled primers, labelled nucleotides and gel-electrophoresis [21]. The methodological performance of Pyrosequencng in determination of difficult secondary DNA Current Pyrosequencing strategy using a commercial machine allows more than 50 nucleotides to be de novo sequenced routinely. Pyrosequencing may be the method of choice for sequencing of difficult secondary DNA structures which cannot be sequenced by conventional sequencing. In this review we discuss the use of Pyrosequencing for mutation scanning, SNP scanning and haplotyping, and describe the cost reduction efforts for largescale studies. Re-sequencing for mutation discoveryThe ability to sequence a large number of DNA samples rapidly and accurately for detection of all possible mutations is a critical goal in biomedicine. DNA mutations can be classified as known or unknown mutations. If the mutation is known, the region containing the mutation can be analyzed at or nearby the mutation site. If the mutation is unknown, re-sequencing of the region for determination of the nature of the mutation is required. When DNA from biopsy material is being resequenced, a quantitative method for determining the ratio between wild and mutated template is desired. When analyzin...

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An oligonucleotide hybridization approach to DNA sequencing

Cited by 228 publications

References 4 publications

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

DNA sequencing by hybridization with additional information available

Discovery of single nucleotide polymorphisms and mutations by Pyrosequencing

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