DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes

Farag, Nada; Ercolani, Gianfranco; Grosso, Erica Del; Ricci, Francesco

doi:10.1002/anie.202208367

Cited by 19 publications

(12 citation statements)

References 62 publications

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“…More specifically, as a degrading enzyme, we selected Uracil‐DNA Glycosylase (UDG), a DNA repair enzyme belonging to the family of base excision repair (BER) that hydrolyses deoxyuridine mutations from ssDNA or dsDNA strands leading to the formation of abasic sites. [ 36,37 ] We have then designed a Cy3‐conjugated strand in which 4 deoxyuridine lesions are uniformly distributed along the sequence ( Figure a). The enzymatic activity of UDG on the mutated bases creates abasic sites where deoxyuridine lesions are present inducing the spontaneous de‐hybridization of the strand and its downstream substitution by a replacing unmodified DNA strand labeled with a Cy5 fluorophore (Figure 3b).…”

Section: Resultsmentioning

confidence: 99%

Dynamic and Reversible Decoration of DNA‐Based Scaffolds

et al. 2023

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usually proceeds through the formation of non-covalent reversible interactions, they can also be designed to undergo a change in their structural configuration or functionality in response to multiple chemical and environmental stimuli. [15,16] Rational and programmable control of these supramolecular functional bio-scaffolds remain, however, challenging, and it is often difficult to achieve higher-order organization of multiple labeling groups in a versatile and dynamic way.Compared to other biomolecules employed for the self-assembly of structures and scaffolds, the use of synthetic DNA as a building block presents several advantages. First, the predictable and programmable nature of DNA-DNA base pairing allows the rational design of DNAbased structures with well-defined 2D and 3D geometry. [17,18] Second, the sequencespecific addressability of DNA strands together with the possibility to covalently attach different functional moieties on the backbone of a DNA oligonucleotide permits the controlled nanoscale decoration at specific locations on the DNA structure with several molecular labels. The above features have been successfully exploited in the last years to make DNA-based scaffolds decorated with a variety of different chemical and biological species such as antibodies, [19,20] signaling moieties, [21,22] aptamers, [23,24] virus capsids, [25,26] and proteins [27,28] that have found applications in bioimaging, drug delivery, and cancer therapeutics. [21,29,30] Despite the above examples clearly illustrating the versatility of synthetic DNA as building blocks to create molecular bio-scaffolds, the methods employed so far for the decoration of DNA-based assemblies often lack versatility and programmability, they are "static" and do not allow the replacement of the labels "on the fly" without prior structure disassembly. Developing novel approaches to control the decoration and labeling of DNA scaffolds with multiple functional moieties in a dynamic way will allow for achieving functional biomaterials with improved adaptability, precision, and sensing capabilities.Motivated by the above arguments, we demonstrate here a strategy to achieve dynamic and site-specific decoration of DNAbased scaffolds. To do so, we employed a model scaffold system DNA structure formed through the self-assembly of DNA tiles. More specifically, we have employed anti parallel double-crossover DNA tiles (DAE-E) formed through the hybridization of five different DNA strands. [31][32][33] These tiles display 4 singlestranded sticky ends (each of 5 nucleotides) that induce their An approach to achieving dynamic and reversible decoration of DNA-based scaffolds is demonstrated here. To do this, rationally engineered DNA tiles containing enzyme-responsive strands covalently conjugated to different molecular labels are employed. These strands are designed to be recognized and degraded by specific enzymes (i.e., Ribonuclease H, RNase H, or Uracil DNA Glycosylase, UDG) inducing their spontaneous de-hybridization from the assembled tile and rep...

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Section: Resultsmentioning

confidence: 99%

Dynamic and Reversible Decoration of DNA‐Based Scaffolds

et al. 2023

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“…The amplification module was constructed by the Bst DNA polymerase large fragment (hereinafter referred to as Bst polymerase) and Nt.AlwI, which exponentially amplified the nRT-cDNA into the nicked amplified product (nAmP) for the initiation of the signal output module. The last module was constructed by uracil-DNA glycosylase (UDG) and endonuclease IV (endo IV), which truncated the output fluorescent substrate (OFS) and released a fluorescent signal by mimicking the base excision repair (BER) process. , Each module had an amplified function and could work independently or in assembly. The RT-NExT was able to detect 10 –18 M target tsRNA in 10 min with a linear range of 7 orders of magnitude.…”

Section: Introductionmentioning

confidence: 99%

Modularized Enzymatic Tandem Reaction for tsRNA Detection

et al. 2022

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tRNA-derived small RNA (tsRNA) has emerged as a new biomarker for early diagnosis and prognosis prediction of breast cancer. Like the detection of other small non-coding RNAs, the traditional DNA circuit could be used for the tsRNA detection. However, the highly coupling DNA strands in the circuit increase the difficulty of design and could raise a false-positive signal. Here, we demonstrated a versatile modularized enzymatic tandem reaction, namely, reverse-transcribed nicking exponential truncation (RT-NExT). This enzymatic reaction was constructed by cohesive modules, which can work independently or in assembly. Each module could amplify and initiate the downstream module. The RT-NExT reaction could detect 10 −18 M ts-66 or ts-86 within 10 min and exhibited excellent consistency to the qRT-PCR when measuring the tsRNA expression level of breast cancer or healthy patients. RT-NExT provides an appealing detection strategy for further research on the clinical diagnosis with tsRNAs.

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“…Owing to its robustness, programmability, and recognition capabilities, DNA can alter its structure in response to external stimuli, including temperature, [9a,16] light, [17] redox agents, [18] pH, [17a,19] and enzymes. [20] Often, these stimuli are employed to modify the nanoscopic structure of DNA nanomaterials under thermodynamic control. [21] Developing technologies that alter the energy landscape of self-assembly over time allows the operation of non-equilibrium systems.…”

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Light‐Activated Assembly of DNA Origami into Dissipative Fibrils

Berg,

Berengut,

Bai

et al. 2023

Angew Chem Int Ed

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Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A‐motif—protonated, self‐complementary poly(adenine) sequences—can propagate DNA origami into one‐dimensional, micron‐length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste‐free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well‐defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A‐motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non‐equilibrium nanotechnology.

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DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes

Cited by 19 publications

References 62 publications

Dynamic and Reversible Decoration of DNA‐Based Scaffolds

Dynamic and Reversible Decoration of DNA‐Based Scaffolds

Modularized Enzymatic Tandem Reaction for tsRNA Detection

Light‐Activated Assembly of DNA Origami into Dissipative Fibrils

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