Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system.

Walker, G. Terrance; Little, Michael C.; Nadeau, James G.; Shank, D.

doi:10.1073/pnas.89.1.392

Cited by 468 publications

(228 citation statements)

References 20 publications

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“…However, there are special needs for DNA nanotechnology or circuitry that few existing methods meet. We therefore decided to use a modified version of strand displacement amplification (SDA) (24,25). SDA is an amplification method based on continuous nicking of a dsDNA (by a sequence-specific nicking enzyme) and primer extension from the nicked site (by a DNA polymerase with strong strand-displacement activity).…”

Section: Resultsmentioning

confidence: 99%

Stacking nonenzymatic circuits for high signal gain

Chen

Briggs

McLain

et al. 2013

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

223

217

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Signal amplification schemes that do not rely on protein enzymes show great potential in areas as abstruse as DNA computation and as applied as point-of-care molecular diagnostics. Toeholdmediated strand displacement, a programmable form of dynamic DNA hybridization, can be used to design powerful amplification cascades that can achieve polynomial or exponential amplification of input signals. However, experimental implementation of such amplification cascades has been severely hindered by circuit leakage due to catalyst-independent side reactions. In this study, we systematically analyzed the origins, characteristics, and outcomes of circuit leakage in amplification cascades and devised unique methods to obtain high-quality DNA circuits that exhibit minimal leakage. We successfully implemented a two-layer cascade that yielded 7,000-fold signal amplification and a two-stage, four-layer cascade that yielded upward of 600,000-fold signal amplification. Implementation of these unique methods and design principles should greatly empower molecular programming in general and DNA-based molecular diagnostics in particular.amplifier | enzyme-free | DNA circuitry S ignal amplification is a ubiquitous theme in biology and engineering, and the ability to amplify signals at the molecular level in large measure determines the complexity and robustness of the molecular devices and systems that can be built. Over the past decade, DNA has been established as the ultimate "intelligent material" to build complex structures, circuits, and devices. DNA circuits have been integrated to form complex Boolean networks (1) and molecular neural networks (2). Such programmed circuits have begun to have applications in ordered chemical synthesis (3, 4), multiplexed labeling of biomolecules for fluorescent microscopy (5, 6), and detection of both nucleic acid and nonnucleic acid analytes (7-9). The combination of DNA circuitry and DNA nanotechnology (10, 11) has given rise to DNA robotics (12) and assembly lines (13).The signal amplifiers underlying many of these advances are metastable DNA substrates whose conformational transformations can be catalytically triggered by strand displacement. The first amplifier of this class was designed by Turberfield et al. (14) and was later modified by Seelig et al. by using metastable kissingloop structures (15). Since then, many hybridization-based catalytic systems have been developed, including ones based on topologically constrained interactions (16), entropy-driven strand exchange (17), and catalyzed hairpin assembly (CHA) (18). Some of these schemes allow cascading of catalysis wherein the product of one reaction serves as the catalyst of another reaction. Autocatalytic reactions (17, 19) and cross-catalytic reactions (18) may also be constructed and programmed. Such molecular amplifiers can guard against signal damping during serial signal transductions in nucleic acid circuits and are easily adapted to the integration of logical operations (20).Whereas the outcome of these amplifiers, the ampl...

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Section: Resultsmentioning

confidence: 99%

Stacking nonenzymatic circuits for high signal gain

Chen

Briggs

McLain

et al. 2013

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

223

217

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“…In addition to the widely used PCR-based detection (1,2), several amplification methods have been invented. They include nucleic acid sequence-based amplification (NASBA) (3), self-sustained sequence replication (3SR) (4) and strand displacement amplification (SDA) (5,6). Each of these amplification methods has its own innovation to re-initiate new rounds of DNA synthesis.…”

Section: Introductionmentioning

confidence: 99%

Loop-mediated isothermal amplification of DNA

Notomi¹

2000

Nucleic Acids Research

7,023

5,962

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We have developed a novel method, termed loopmediated isothermal amplification (LAMP), that amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions. This method employs a DNA polymerase and a set of four specially designed primers that recognize a total of six distinct sequences on the target DNA. An inner primer containing sequences of the sense and antisense strands of the target DNA initiates LAMP. The following strand displacement DNA synthesis primed by an outer primer releases a single-stranded DNA. This serves as template for DNA synthesis primed by the second inner and outer primers that hybridize to the other end of the target, which produces a stem-loop DNA structure. In subsequent LAMP cycling one inner primer hybridizes to the loop on the product and initiates displacement DNA synthesis, yielding the original stem-loop DNA and a new stem-loop DNA with a stem twice as long. The cycling reaction continues with accumulation of 10 9 copies of target in less than an hour. The final products are stem-loop DNAs with several inverted repeats of the target and cauliflower-like structures with multiple loops formed by annealing between alternately inverted repeats of the target in the same strand. Because LAMP recognizes the target by six distinct sequences initially and by four distinct sequences afterwards, it is expected to amplify the target sequence with high selectivity.

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“…Few if any studies have been published comparing different methods, but linker mediated approaches appear to dominate the recent literature. Further improvements in specificity and yield might also be achieved by combining different portions of the above methods or adapting some of these to use non-PCR methods of amplification (such as strand displacement amplification (SDA), rolling-circle amplification (RCA) and multiple-displacement amplification (MDA) (Walker et al, 1992;Lizardi et al, 1998;Dean et al, 2002).…”

Section: Advances In Cloning Of Insertion Sitesmentioning

confidence: 99%

Retroviral insertional mutagenesis: past, present and future

et al. 2005

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Retroviral insertion mutagenesis screens in mice are powerful tools for efficient identification of oncogenic mutations in an in vivo setting. Many oncogenes identified in these screens have also been shown to play a causal role in the development of human cancers. Sequencing and annotation of the mouse genome, along with recent improvements in insertion site cloning has greatly facilitated identification of oncogenic events in retrovirus-induced tumours. In this review, we discuss the features of retroviral insertion mutagenesis screens, covering the mechanisms by which retroviral insertions mutate cellular genes, the practical aspects of insertion site cloning, the identification and analysis of common insertion sites, and finally we address the potential for use of somatic insertional mutagens in the study of nonhaematopoietic and nonmammary tumour types.

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Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system.

Cited by 468 publications

References 20 publications

Stacking nonenzymatic circuits for high signal gain

Stacking nonenzymatic circuits for high signal gain

Loop-mediated isothermal amplification of DNA

Retroviral insertional mutagenesis: past, present and future

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