A Locked Nucleic Acid-Based Nanocrawler: Designed and Reversible Movement Detected by Multicolor Fluorescence

Astakhova, Kira; Pasternak, Karol; Campbell, Meghan A.; Gupta, Pankaj; Wengel, Jesper

doi:10.1021/ja311250w

Cited by 20 publications

(23 citation statements)

References 22 publications

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“…To date, hybridisation of DNA and RNA targets by short oligonucleotide probes is assessed by using thermal denaturation experiments, which provide a midpoint of duplex denaturation, called a melting temperature ( T m ). The T m value is used to compare target recognition by different strands and to select the most appropriate probe for, for example, polymerase chain reaction (PCR), sequencing, or amplification of free nucleic acid targeting . However, besides sequence content, the T m value is a function of several other parameters, such as strand concentration, salt concentration, microenvironment, and pH .…”

Section: Introductionmentioning

confidence: 99%

Improving the Design of Synthetic Oligonucleotide Probes by Fluorescence Melting Assay

et al. 2018

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Nucleic acid hybridisation plays a key role in many biological processes, including transcription, translation, and regulation of gene expression. Several sophisticated applications rely on this fundamental interaction, including the polymerase chain reaction, sequencing, and gene therapy. To target a nucleic acid sequence specifically, synthetic oligonucleotides with a suitable affinity and specificity towards the target need to be designed. The affinity of potential probes or therapeutic agents to their target sequence is generally investigated by melting experiments, which break the hydrogen-bonding and stacking interactions that stabilise the double helix resulting in the formation of two single strands. In this paper, we report a comparative study of hybridisation for short fluorescent oligonucleotides labelled with cyanine and ATTO dyes, performed by the currently used UV melting assay and by a more sensitive fluorescence melting experiment. Using different oligonucleotide sequences in the concentration range of 5 nm to 2 μm, we observed a stabilising effect of the fluorophores on the duplexes, especially at low concentrations. We paid particular attention to the effect of polycations and to molecular crowding as major parameters that define the stability and the geometry of nucleic acid duplexes in biological samples. We also demonstrated how the fluorometry-based melting data could aid the design of a probe targeting a human BRAF gene fragment to reduce the off-target binding by a factor of seven.

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Section: Introductionmentioning

confidence: 99%

Improving the Design of Synthetic Oligonucleotide Probes by Fluorescence Melting Assay

et al. 2018

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“…The nanocrawler system in Figure 25 showed directional movement along a complementary DNA road. 180 The nanocrawler (46 nucleotides in total) is formed from DNA, LNA, and 2¤-amino-LNA bearing a pyrene derivative (see section 2.1.2). The lengths of the stations on the DNA road increase in the 5¤ ¼ 3¤ direction of the road (6, 9, 12, and 15 nucleotides at stations 14, respectively) to make the duplex of the crawler with the station more stable in this order.…”

Section: Determination Of Dna Nanostructures In Solutionsmentioning

confidence: 99%

Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics

Komiyama

Yoshimoto

Sisido

et al. 2017

Bulletin of the Chemical Society of Japan

275

131

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In this review, we introduce two kinds of bio-related nanoarchitectonics, DNA nanoarchitectonics and cellmacromolecular nanoarchitectonics, both of which are basically controlled by chemical strategies. The former DNA-based approach would represent the precise nature of the nanoarchitectonics based on the strict or "digital" molecular recognition between nucleic bases. This part includes functionalization of single DNAs by chemical means, modification of the main-chain or side-chain bases to achieve stronger DNA binding, DNA aptamers and DNAzymes. It also includes programmable assemblies of DNAs (DNA Origami) and their applications for delivery of drugs to target sites in vivo, sensing in vivo, and selective labeling of biomaterials in cells and in animals. In contrast to the digital molecular recognition between nucleic bases, cell membrane assemblies and their interaction with macromolecules are achieved through rather generic and "analog" interactions such as hydrophobic effects and electrostatic forces. This cell-macromolecular nanoarchitectonics is discussed in the latter part of this review. This part includes bottom-up and top-down approaches for constructing highly organized cell-architectures with macromolecules, for regulating cell adhesion pattern and their functions in twodimension, for generating three-dimensional cell architectures on micro-patterned surfaces, and for building synthetic/natural macromolecular modified hybrid biointerfaces.

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“…Thus, synthetic nucleic acids, such as Peptide Nucleic Acid (PNA) and Locked Nucleic Acid (LNA) (Fig. 6A), are being used as alternatives, for example, to the classical ssDNAbased capture probes [147,148]. Briefly, PNAs are synthetic DNA analogs whose sugar phosphate backbone has been replaced by an uncharged N-(2-aminoethyl) glycine scaffold.…”

Section: Nucleic Acids In Biosensing With Fo and Pwgmentioning

confidence: 99%

Fluorescence based fiber optic and planar waveguide biosensors. A review

Benito‐Peña

Valdés

Glahn-Martínez

et al. 2016

Analytica Chimica Acta

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The application of optical biosensors, specifically those that use optical fibers and planar waveguides, has escalated throughout the years in many fields, including environmental analysis, food safety and clinical diagnosis. Fluorescence is, without doubt, the most popular transducer signal used in these devices because of its higher selectivity and sensitivity, but most of all due to its wide versatility. This paper focuses on the working principles and configurations of fluorescence-based fiber optic and planar waveguide biosensors and will review biological recognition elements, sensing schemes, as well as some major and recent applications, published in the last ten years. The main goal is to provide the reader a general overview of a field that requires the joint collaboration of researchers of many different areas, including chemistry, physics, biology, engineering, and material science.

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A Locked Nucleic Acid-Based Nanocrawler: Designed and Reversible Movement Detected by Multicolor Fluorescence

Cited by 20 publications

References 22 publications

Improving the Design of Synthetic Oligonucleotide Probes by Fluorescence Melting Assay

Improving the Design of Synthetic Oligonucleotide Probes by Fluorescence Melting Assay

Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics

Fluorescence based fiber optic and planar waveguide biosensors. A review

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