Dendritic Nucleic Acid Structures

Nilsen, Thor W.; Grayzel, Joseph; Prensky, Wolf

doi:10.1006/jtbi.1997.0446

Cited by 124 publications

(101 citation statements)

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“…A defining feature of DNA nanotechnology is the ability of DNA single strands to bind selectively only with complementary strands (1)(2)(3)(4)(5)(6)(7)(8). Identical particles coated with identical DNA strands can be joined together by adding to the suspension a linker strand that attaches to the two coatings (9,10).…”

Section: Multifunctional | Thermodynamicsmentioning

confidence: 99%

Polygamous particles

Feng

Sha

et al. 2012

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

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DNA is increasingly used as an important tool in programming the self-assembly of micrometer-and nanometer-scale particles. This is largely due to the highly specific thermoreversible interaction of cDNA strands, which, when placed on different particles, have been used to bind precise pairs in aggregates and crystals. However, DNA functionalized particles will only reach their true potential for particle assembly when each particle can address and bind to many different kinds of particles. Indeed, specifying all bonds can force a particular designed structure. In this paper, we present the design rules for multiflavored particles and show that a single particle, DNA functionalized with many different "flavors," can recognize and bind specifically to many different partners. We investigate the cost of increasing the number of flavors in terms of the reduction in binding energy and melting temperature. We find that a single 2-μm colloidal particle can bind to 40 different types of particles in an easily accessible time and temperature regime. The practical limit of ∼100 is set by entropic costs for particles to align complementary pairs and, surprisingly, by the limited number of distinct "useful" DNA sequences that prohibit subunits with nonspecific binding. For our 11 base "sticky ends," the limit is 73 distinct sequences with no unwanted overlaps of 5 bp or more. As an example of phenomena enabled by polygamous particles, we demonstrate a three-particle system that forms a fluid of isolated clusters when cooled slowly and an elastic gel network when quenched. multifunctional | thermodynamicsA defining feature of DNA nanotechnology is the ability of DNA single strands to bind selectively only with complementary strands (1-8). Identical particles coated with identical DNA strands can be joined together by adding to the suspension a linker strand that attaches to the two coatings (9, 10). Such structures have been used for immunoassays (11), particle aggregation, and formation of crystalline structures, typically Face Centered Cubic (FCC) (12). Use has also been made of different particles, A and B, functionalized with cDNA strands (13). This configuration, where A-A and B-B bonds do not occur but A-B bonds do (14-16), has been exploited to form more complex crystals, such as BCC or CsCl structures (12,17). Over the past several years, there has been a great deal of progress in modeling the DNA-mediated interparticle interaction and making quantitative comparisons with experiments (16,(18)(19)(20)(21)(22)(23). Although nanoscale particles are typically coated with tens to hundreds of DNA molecules, and micrometer-scale colloids can be coated with 10 4 -10 5 DNA strands, there has been little work on coating particles with more than one type of DNA sequence on the same particle. Allowing these particles to be "polygamous," to specifically bind to a particular set of other particles, enables not only the fabrication of more complex crystals but the design of more general programmed structures. For rigid structures,...

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Section: Multifunctional | Thermodynamicsmentioning

confidence: 99%

Polygamous particles

Feng

Sha

et al. 2012

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

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“…Polymeric matrices allow the attachment of multiple SACs, making them an attractive platform for generating polyvalent substrate molecules. Different types of polymeric matrices comprised of DNA itself have been described (20,27,28). These polymeric or dendritic DNA structures have been used to amplify radioactive or fluorescent signals by direct incorporation of label in hybridization-based detection (28)(29)(30).…”

Section: Resultsmentioning

confidence: 99%

“…wt 1.2 × 10 8 g/mol) and 8-layer (mol. wt 1.2 × 10 9 g/mol) DNA dendrimers were prepared at Genisphere Inc. as previously described (20,21). Briefly, DNA dendrimers were assembled from seven oligonucleotides, strands 1-7.…”

Section: Dna Dendrimersmentioning

confidence: 99%

“…The method described here allows the detection of oligonucleotide cassette molecules with two polymerase reaction sites at low attomole levels. Attachment of oligonucleotide cassettes onto a DNA-based polymeric support called a 3D DNA dendrimer (20,21) further enhanced the sensitivity. These modified dendrimers represent molecular hubs consisting of thousands of reactive centers that accommodate a DNA polymerase to generate PPi through catalytic amplification.…”

Section: Introductionmentioning

confidence: 99%

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Signal amplification through nucleotide extension and excision on a dendritic DNA platform

Capaldi

Getts²,

Jayasena³

2000

Nucleic Acids Research

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Techniques that provide strong signal amplification are useful in diagnostic applications, especially in detecting low concentrations of non-amplifiable target molecules. A versatile and strong signal amplification method based on activities of a DNA polymerase to generate high concentrations of pyrophosphate (PPi) is described. The generation of PPi is catalyzed by nucleotide extension and excision activities of a DNA polymerase on an oligonucleotide cassette. The signal is generated upon enzymatic conversion of PPi to ATP and ATP levels subsequently detected with firefly luciferase. Bioluminesence produced by an oligonucleotide cassette consisting of just two polymerase reaction sites is sufficient to detect them at low attomole levels. The attachment of a large number of these oligonucleotide cassettes to DNA dendrimers enabled the detection of such polyvalent substrate molecules at low zeptomole (10 -21 mol) concentrations. The extent of signal amplification obtained with dendrimer substrates is comparable to exponential target amplifications provided by nucleic acid amplification methods. The attachment of such PPi-generating dendritic DNA platforms to ligands that mediate target recognition would potentially permit detection of extremely low concentrations of analytes in diagnostic assays.

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“…Probes can be labeled using two other methods known as (1) amino-allyl dye coupling or postlabeling (Randolph and Waggoner, 1997) (Amersham Biosciences) and (2) 3D labeling with dendritic nucleic acid structure (Nilsen et al, 1997;Stears et al, 2000) (Genisphere, Hatfield, PA). In our experience, the postlabeling method works as well as the direct labeling method.…”

Section: Probe Purificationmentioning

confidence: 99%

Methods for Genome-Wide Analysis of Gene Expression Changes in Polyploids

Wang

Lee²,

Tian³

et al. 2005

Methods in Enzymology

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Polyploidy is an evolutionary innovation, providing extra sets of genetic material for phenotypic variation and adaptation. It is predicted that changes of gene expression by genetic and epigenetic mechanisms are responsible for novel variation in nascent and established polyploids (Liu and Wendel, 2002;Osborn et al., 2003;Pikaard, 2001). Studying gene expression changes in allopolyploids is more complicated than in autopolyploids, because allopolyploids contain more than two sets of genomes originating from divergent, but related, species. Here we describe two methods that are applicable to the genome-wide analysis of gene expression differences resulting from genome duplication in autopolyploids or interactions between homoeologous genomes in allopolyploids. First, we describe an amplified fragment length polymorphism (AFLP)-complementary DNA (cDNA) display method that allows the discrimination of homoeologous loci based on restriction polymorphisms between the progenitors. Second, we describe microarray analyses that can be used to compare gene expression differences between the allopolyploids and respective progenitors using appropriate experimental design and statistical analysis. We demonstrate the utility of these two complementary methods and discuss the pros and cons of using the methods to analyze gene expression changes in autopolyploids and allopolyploids. Furthermore, we describe these methods in general terms to be of wider applicability for comparative gene expression in a variety of evolutionary, genetic, biological, and physiological contexts.

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Dendritic Nucleic Acid Structures

Cited by 124 publications

References 0 publications

Polygamous particles

Polygamous particles

Signal amplification through nucleotide extension and excision on a dendritic DNA platform

Methods for Genome-Wide Analysis of Gene Expression Changes in Polyploids

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