Considerations of Solid-Phase DNA Amplification

Palanisamy, Ramkumar; Connolly, Ashley R.; Trau, Matt

doi:10.1021/bc900491s

Cited by 29 publications

(36 citation statements)

References 29 publications

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“…We have found that the restriction reaction depends on the DNA density, and have demonstrated the existence of a threshold above which the reaction is inhibited (essentially in a stepwise manner) 20 . This result, which has been later confirmed by other groups [21][22][23] , suggests that the accessibility of dsDNA molecules in these surface-bound brushy matrices critically depends on the inherent steric hindrance.…”

supporting

confidence: 66%

“…The side-access effect reported in this study has not been hitherto described, although other investigations demonstrated enzymatic reactions on surface-bound DNA molecules 6,[21][22][23][38][39][40][41][42][43][44] . These studies used either longer dsDNA molecules 23,40 or molecules provided with significantly less-rigid surface linkers and/ or different chemical strategies for DNA self-assembly 6,23,39,41 .…”

Section: Discussionmentioning

confidence: 45%

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Two-dimensional enzyme diffusion in laterally confined DNA monolayers

et al. 2011

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Addressing the effects of confinement and crowding on biomolecular function may provide insight into molecular mechanisms within living organisms, and may promote the development of novel biotechnology tools. Here, using molecular manipulation methods, we investigate restriction enzyme reactions with double-stranded (ds)DnA oligomers confined in relatively large (and flat) brushy matrices of monolayer patches of controlled, variable density. We show that enzymes from the contacting solution cannot access the dsDnAs from the topmatrix interface, and instead enter at the matrix sides to diffuse two-dimensionally in the gap between top-and bottom-matrix interfaces. This is achieved by limiting lateral access with a barrier made of high-density molecules that arrest enzyme diffusion. We put forward, as a possible explanation, a simple and general model that relates these data to the steric hindrance in the matrix, and we briefly discuss the implications and applications of this strikingly new phenomenon.

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supporting

confidence: 66%

Section: Discussionmentioning

confidence: 45%

Two-dimensional enzyme diffusion in laterally confined DNA monolayers

et al. 2011

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“…Access of DpnII (a homodimer) to the monolayer (density~1 Â 10 12 molecules/cm 2 ) is fully inhibited when the average dsDNA-dsDNA distance <10 nm, which also corresponds to the diameter of the DpnII holoenzyme. This result, also supported by other studies (Bar and Bar-Ziv 2009;McCalla et al 2009;Palanisamy et al 2010), indicates that accessibility of protein binding sites in dsDNA molecules confined in self-assembled nanostructures critically depends on the steric constraints imposed by the molecular density. In contrast to previous studies demonstrating that macromolecular crowding significantly affects the speed of endonuclease processing on DNA substrates (Sasaki et al 2007), this work provides a demonstration that the enzymatic processing is either fully allowed or fully inhibited as a function of molecular density.…”

Section: Enzymatic Reactions Within Nanoconfined Nucleic Acid Architesupporting

confidence: 84%

Emergent Properties and Functions of Nanoconfined Nucleic Acid Architectures

et al. 2015

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The facile ability of DNA to self-assemble has enabled the creation of complex architectures with diverse functions on surfaces or in solution. This approach provides a powerful design tool for the development of nanoscale devices with transformative applications in multiple areas, including the detection of complex biomolecules, drug delivery, and in situ biomolecular synthesis. However, little is known of the effect of confinement on the function of complex nucleic acid architectures, which exhibit unanticipated behaviors that presumably reflect high-level molecular crowding. In this chapter, we review selected recent studies that describe the application and atypical behaviors of nanoconfined nucleic acids, in particular with respect to hybridization, denaturation, conformation, stability, and enzyme accessibility. We argue that the novel behavior of dense nucleic acid arrays naturally emerge as a result of immobilization and reduction in spatial degrees of freedom. We summarize by emphasizing the need for basic physical–chemical studies of dense nucleic acid architectures, involving an interplay of experimental and theoretical approaches, in order to effectively guide the successful technological development of nucleic acid nanodevices

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“…PCR can performed in a solution, using immobilized amplicon at solid phase (SP-PCR) [93,94] or compartmentalization of template molecules in water droplets in a water-in-oil emulsion (Em-PCR) [92,95,96] to obtain the desired sequence or fragment length of sample DNA. The combination of improvements in chemistry and the evolution in analytical-separation, detection-platforms provides a plethora of applications.…”

Section: Extraction Of Compound And/or Challenging Samplesmentioning

confidence: 99%

Forensic DNA Technological Advancements as an Emerging Perspective on Medico-Legal Autopsy: A Mini Review

Pádár¹,

Zenke²,

Kozma³

2018

Post Mortem Examination and Autopsy - Current Issues From Death to Laboratory Analysis

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The importance of biological traces and evidences related to a criminal matter has been recognized for a long time. The examination of the expression of genetic polymorphism has been an integral part of the multidisciplinary field of medico-legal autopsy for over a century. Since the initial application of blood group antigens for personalization of a putative perpetrator in a murder case, the discipline of forensic genetics has evolved as a standard of forensic sciences. The real breakthrough, the application of molecular tools and processes for the in-vitro replication of genetic substances, has increasingly allowed the exploitation of advances of molecular genetics for both forensic and criminal investigations. Although there are certainly many more applications and scientific fields in the medico-legal arena, the relatively fast progress of genetics, which has accelerated recently with state-of-art technologies, can provide ever more relevant information in relation to a corpse or the cause and manner that resulted in the corpse for autopsy. This topic concerns the currently accepted forensic DNA technology, and the last section reviews commonly used markers for nuclear and mitochondrial DNA analysis as well as ongoing research. This review also focuses on the increasingly important non-human sources of DNA, and shortly covers the main aspects of animal forensic DNA examination.

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Considerations of Solid-Phase DNA Amplification

Cited by 29 publications

References 29 publications

Two-dimensional enzyme diffusion in laterally confined DNA monolayers

Two-dimensional enzyme diffusion in laterally confined DNA monolayers

Emergent Properties and Functions of Nanoconfined Nucleic Acid Architectures

Forensic DNA Technological Advancements as an Emerging Perspective on Medico-Legal Autopsy: A Mini Review

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