Sequencing of megabase plus DNA by hybridization: Theory of the method

Drmanac, Radoje; Labat, Ivan; Brukner, Ivan; Crkvenjakov, Radomir

doi:10.1016/0888-7543(89)90290-5

Cited by 330 publications

(119 citation statements)

References 27 publications

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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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“…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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“…Also, large scale sequencing using hybridization of genomic DNA fragments to an array of oligomers (e.g. all 65 536 octamers) has been proposed [3,4]. All these methods, but also standard procedures like the polymerase chain reaction, for instance, would gain from an improvement in duplex stability of oligonucleotides.…”

Section: Introductionmentioning

confidence: 99%

Quantitative measurements on the duplex stability of 2,6‐diaminopurine and 5‐chloro‐uracil nucleotides using enzymatically synthesized oligomers

1990

FEBS Letters

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2,6‐Diaminopurine and 5‐chloro‐uracil 2'‐deoxynucleoside 5'‐triphosphates were synthesized from their 2'‐deoxynucleosides. Using a method of creating oligonucleotides by enzymatic primer extension, dodecanucleotides representing an XbaI/SalI site and the complementary SalI/XbaI site were generated containing these base modifications. Their duplex stability was quantitatively compared by thin‐layer chromatography to oligomers containing 2'‐deoxyadenosine and 2'‐deoxythymidine. The two unmodified oligomers already showed significant differences in dissociation temperature and binding equilibrium. Substitution with 5‐chloro‐2'‐deoxyuridine did not affect the dissociation temperature of either oligomer, the 2,6‐diaminopurine, however, led to an increase of 1.8°C or 1.5°C per modified base, respectively. While in the XbaI/SalI oligomer both base modifications changed the binding equilibrium, the 2,6‐diaminopurine by a factor of 1.32, the 5‐chloro‐uracil by 0.65, no such effect was found with the complementary oligomer.

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“…However, the reliance on capillary electrophoresis means that conventional sequencing is not likely to become a particularly low-cost, high-speed, or high-throughput technique. The advent of next-generation sequencing, based on massively parallel arrays of individual sequencing reactions, has drastically improved the sequencing throughput and greatly reduced cost and time [2][3][4][5][6][7]. High-throughput pyrosequencing [8], relying on detection of chemiluminescence signals generated from millions of DNA polymerization reactions, has shown excellent accuracy, with longer read lengths than those available with other next-generation technologies, and has been successfully used for de novo sequencing, resequencing, and metagenomic sequencing [9][10][11][12][13].…”

mentioning

confidence: 99%

Improved picoliter-sized micro-reactors for high-throughput biological analysis

Han

Yuan

Wei

et al. 2013

Sci. China Life Sci.

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High-throughput pyrosequencing, carried out in millions of picoliter-sized reactors on a fiber-optic slide, is known for its longer read length. However, both optical crosstalk (which reduces the signal-to-noise ratio of CCD images) and chemical retention adversely affect the accuracy of chemiluminescence determination, and ultimately decrease the read length and the accuracy of pyrosequencing results. In this study, both titanium and oxidized aluminum films were deposited on the side walls and upper faces of micro-reactor slides to enhance optical isolation; the films reduced the inter-well crosstalk by one order of magnitude. Subsequently, chemical retention was shown to be caused by the lower diffusion coefficient of the side walls of the picolitersized reactors because of surface roughness and random pores. Optically isolated fiber-optic slides over-coated with silicon oxide showed smoother surface morphology, resulting in little chemical retention; this was further confirmed with theoretical calculations. Picoliter-sized micro-reactors coated with titanium-silicon oxide films showed the least inter-well optical crosstalk and chemical retention; these properties are expected to greatly improve the high-throughput pyrosequencing performance.high throughput analysis, picoliter-sized micro-reactor, surface coating Citation:Han W J, Yuan L N, Wei Q Q, et al. Improved picoliter-sized micro-reactors for high-throughput biological analysis.

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Sequencing of megabase plus DNA by hybridization: Theory of the method

Cited by 330 publications

References 27 publications

DNA sequencing by hybridization with additional information available

DNA sequencing by hybridization with additional information available

Quantitative measurements on the duplex stability of 2,6‐diaminopurine and 5‐chloro‐uracil nucleotides using enzymatically synthesized oligomers

Improved picoliter-sized micro-reactors for high-throughput biological analysis

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