Rolling Circle Amplification-Templated DNA Nanotubes Show Increased Stability and Cell Penetration Ability

Hamblin, Graham D.; Carneiro, Karina M. M.; Fakhoury, Johans; Bujold, Katherine E.; Sleiman, Hanadi F.

doi:10.1021/ja2107492

Cited by 185 publications

(160 citation statements)

References 25 publications

Supporting

Mentioning

157

Contrasting

Unclassified

Order By: Relevance

“…Furthermore, improvements in the utility and performance of the method, including its detection sensitivity and speed, may be possible by introducing triple, quadruple, or quintuple amplification with increased numbers of ternary initiation complexes, by modifying ThT-HE and φ29 DNA polymerase, and/or by applying microchannel reactors, 53,54 nanoparticles, 55,56 and electroconductive materials. 57,58 We believe that such refined SATIC-based techniques will enable inexpensive facilitation of various RT-PCR-based assays for diagnosis and inspection, as well as in situ assays for tissues and cells in the near future. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Author Contributions M.K.…”

Section: Resultsmentioning

confidence: 99%

Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes

et al. 2016

View full text Add to dashboard Cite

We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.

show abstract

Section: Resultsmentioning

confidence: 99%

Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes

et al. 2016

View full text Add to dashboard Cite

show abstract

“…One of the applications for these products is as addressable backbones in DNA nanostructures. Work by us 22 and other groups 5,23 has already shown that continuous template strands can help to augment the structural control and biological stability of the resulting products. The repeating A and B sequence domains of ss [10] were chosen to match the binding sites of DNA nanotube rungs that we have previously described (UA and UB) 6 .…”

Section: Resultsmentioning

confidence: 99%

Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds

2015

Self Cite

View full text Add to dashboard Cite

DNA strands of well-defined sequence are valuable in synthetic biology and nanostructure assembly. Drawing inspiration from solid-phase synthesis, here we describe a DNA assembly method that uses time, or order of addition, as a parameter to define structural complexity. DNA building blocks are sequentially added with in-situ ligation, then enzymatic enrichment and isolation. This yields a monodisperse, single-stranded long product (for example, 1,000 bases) with user-defined length and sequence pattern. The building blocks can be repeated with different order of addition, giving different DNA patterns. We organize DNA nanostructures and quantum dots using these backbones. Generally, only a small portion of a DNA structure needs to be addressable, while the rest is purely structural. Scaffolds with specifically placed unique sites in a repeating motif greatly minimize the number of components used, while maintaining addressability. This combination of symmetry and site-specific asymmetry within a DNA strand is easily accomplished with our method.

show abstract

“…In addition to using digested RCR products for assembling DNA nanostructures, applying intact RCR chains is also very popular. For instance, Hamblin et al designed a DNA 'ladder' with RCA generated approximately 1400-15000 bp long ssDNA as the 'strut' and some other DNA oligos as 'rungs', resulting in very high aspect ratio of the final nanotube assembly [12]. Another version of RCR-based nanoassembly is the modified DNA 'origami', in which the generally used virus genomic DNA was replaced with RCR-generated DNA [13] or RNA [14] as the scaffold.…”

Section: Rcr Product Self-assembled Micro-nanoparticlesmentioning

confidence: 99%

Rolling Circle Replication for Engineering Drug Delivery Carriers

Sun

Lü

2015

Ther. Deliv.

View full text Add to dashboard Cite

The technique to generate long concatenated nucleic acids capable of constructing nano-, micro-and macro-scopic structures is a powerful platform for designing drug d elivery carriers.Rolling circle replication (RCR), including DNA and RNA replication, is a process found in some bacteriophages or viroids for replicating the DNA or RNA genomes. In vitro versions of this natural phenomenon are the rolling circle amplification (RCA) [1] and rolling circle transcription (RCT) [2] that enabled cost-efficient synthesis of concatenated DNA and RNA. Φ29 DNA polymerase, the most popular DNA polymerase for RCA, is capable to replicating the full-length genome of Φ29 bacteriophage [3]. The superb RCA performance of Φ29 DNA polymerase is attributed to its high processivity and strand displacement ability, making it possible to generate long consecutive DNA products even in the presence of topologically complicated DNA templates. In addition, Φ29 DNA polymerase reacts in an isothermal condition that obviates the need for a thermal cycler for the reaction. Other isothermal polymerases that can be employed in RCA include Bst DNA polymerase [4], Vent exo-DNA polymerase [1] and so on. For a typical RCA, the three major components are the DNA polymerase, a single stranded DNA (ssDNA) template and a ssDNA primer. The fact that the product is an amplification of the ssDNA template leads to extensive study of RCA for signal amplification in biodetection [1]. Recently, the polymeric property of RCA products has attracted a lot of attention due to the development of DNA nanotechnology [5]. The programmability of the DNA template makes RCA a highly versatile platform to generate DNA particles or gels for biomedical applications. Functional DNA sequences, such as aptamers and DNAzymes, can be incorporated into the RCA products for applications including targeted drug delivery or bioimaging.Similar to RCA, RCT generates periodic RNA products from a ssDNA template. A typical RCT reaction requires only two major components, a DNA-dependent RNA polymerase (generally T7 RNA polymerase) and a ssDNA template containing the binding site of the RNA polymerase [2]. The high programmability of the DNA template makes RCT easy to manipulate. The flexible base-pairing rules of RNA, such as noncanonical base pairing, make RNA nanostructures more versatile and thermally stable than their DNA counterparts, giving RNA protein-like diversity in functions [6]. Functional RNA molecules such as aptamers, ribozyme, miRNA and siRNA have greatly expanded the toolbox for designing RNA carriers for drug delivery.In this editorial, we highlight recent advances in using RCR techniques for engineering DNA-and RNA-based carriers for

show abstract

Rolling Circle Amplification-Templated DNA Nanotubes Show Increased Stability and Cell Penetration Ability

Cited by 185 publications

References 25 publications

Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes

Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes

Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds

Rolling Circle Replication for Engineering Drug Delivery Carriers

Contact Info

Product

Resources

About