A molecular beacon-based DNA switch for reversible pH sensing in vesicles and live cells

Narayanaswamy, Nagarjun; Nair, Raji R.; Suseela, Y. V.; Saini, Deepak Kumar; Govindaraju, T.

doi:10.1039/c6cc02705a

Cited by 25 publications

(24 citation statements)

References 36 publications

(7 reference statements)

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“…An alteration of the physiological pH can be indicative of a diseased condition, and therefore monitoring physiological pH values with high sensitivity is required. Our group designed a molecular beacon (LMB) DNA device appended with a FRET pair as pH sensing probe in cells [19]. The remarkable feature of the LMB probe was the structural transition from a closed (molecular beacon) state to an open (A-motif) state in a pH-responsive manner within artificial vesicles and living cells.…”

Section: Diversity In Dna Nanoarchitecturesmentioning

confidence: 99%

“…Despite the expeditious advancements in the field of DNA nanotechnology, utilization of long DNA sequences, complex computerbased design strategies, reproducibility, and the high cost involved in the entire process have become the limiting factors in the realization of practical applications. In this context, the emerging field of SFM-templated or mutually templated DNA nanotechnology (functional DNA nanoarchitectonics) is considered the state-of-art to construct hybrid DNA nanoarchitectures with assured functional properties and practical applications [12,13,[18][19][20][21]. In functional DNA nanoarchitectonics, short oligonucleotides (ssDNA) with sequences of less than persistence length (ca.…”

Section: Review Introductionmentioning

confidence: 99%

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Molecular architectonics of DNA for functional nanoarchitectures

Ghosh¹,

Datta²,

Govindaraju³

2020

Beilstein J. Nanotechnol.

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DNA is the key biomolecule central to almost all processes in living organisms. The eccentric idea of utilizing DNA as a material building block in molecular and structural engineering led to the creation of numerous molecular-assembly systems and materials at the nanoscale. The molecular structure of DNA is believed to have evolved over billions of years, with structure and stability optimizations that allow life forms to sustain through the storage and transmission of genetic information with fidelity. The nanoscale structural characteristics of DNA (2 nm thickness and ca. 40–50 nm persistence length) have inspired the creation of numerous functional patterns and architectures through noncovalent conventional and unconventional base pairings as well as through mutual templating-interactions with small organic molecules and metal ions. The recent advancements in structural DNA nanotechnology allowed researchers to design new DNA-based functional materials with chemical and biological properties distinct from their parent components. The modulation of structural and functional properties of hybrid DNA ensembles of small functional molecules (SFMs) and short oligonucleotides by adapting the principles of molecular architectonics enabled the creation of novel DNA nanoarchitectures with potential applications, which has been termed as templated DNA nanotechnology or functional DNA nanoarchitectonics. This review highlights the molecular architectonics-guided design principles and applications of the derived DNA nanoarchitectures. The advantages and ability of functional DNA nanoarchitectonics to overcome the trivial drawbacks of classical DNA nanotechnology to fulfill realistic and practical applications are highlighted, and an outlook on future developments is presented.

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Section: Diversity In Dna Nanoarchitecturesmentioning

confidence: 99%

Section: Review Introductionmentioning

confidence: 99%

Molecular architectonics of DNA for functional nanoarchitectures

Ghosh¹,

Datta²,

Govindaraju³

2020

Beilstein J. Nanotechnol.

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“…Narayanaswamy et al proposed alternative adenine-rich oligonucleotide sequences for pH sensors intended to monitor small acidityr anges. [129] Under physiological conditions, the probe adopts ah airpin-like closed state. Protonation of the adenine nucleobases triggers the formation of the extended conformation (A-motif).…”

Section: Host-guestmentioning

confidence: 99%

Synthesis and Supramolecular Functional Assemblies of Ratiometric pH Probes

Méndez‐Ardoy

Reina

Montenegro

2020

Chemistry A European J

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Tracking pH with spatiotemporal resolution is a critical challenge for synthetic chemistry, chemical biology and beyond. Over the last decade, different small probes and supramolecular systems have emerged for in cellulo or in vivo pH tracking. However, pH reporting still presents critical limitations, such as background reduction, improved sensor stability, cell targeting, endosomal escape, near‐ and far‐infrared ratiometric pH tracking and adaption to new imaging techniques (i.e., super‐resolution). These challenges will require the combined efforts of synthetic and supramolecular chemistry working together to develop the next generation of smart materials that will resolve current limitations. Herein, recent advances in the synthesis of small fluorescent probes, together with new supramolecular functional systems employed for pH tracking, are described with an emphasis on ratiometric probes. The combination of organic synthesis and stimuli‐responsive supramolecular functional materials will be essential to solve future challenges of pH tracking, such as improved signal to noise ratio, on target activation and microenvironment reporting.

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“… 4 Unmodified oligonucleotides are also capable of yielding stimuli-responsive DNA structures upon appropriate selection of sequences that can be triggered by several chemical inputs including pH. 5 – 7 Such pH responsive DNA nanostructures have recently attracted much interest in nanomedicine as nanocarriers, for pH-controlled release of drugs, 8 or as nanoprobes capable of tracking pH changes in vitro 9 , 10 and in vivo . 11 Monitoring the alteration of intracellular and/or extracellular pH in vivo can aid the diagnosis and prognosis of several diseases, including cancer.…”

mentioning

confidence: 99%

“… 12 Most of these pH-sensitive DNA-based nanostructures consist of nanostructures decorated with selected fluorophore pairs that exhibit changes in resonance energy transfer in response to changes in pH levels and are often monitored recording their fluorescence emission levels. 6 , 7 , 9 , 10 , 13 Using these all-optical fluorescence measurements results in limited penetration depth and spatial localisation ability due to strong scattering of light in biological tissues. 14 However, with the advent of photoacoustic imaging (PAI), it is now possible to obtain high resolution optical images from greater depths in tissue and to therefore overcome these traditional limitations of all-optical imaging.…”

mentioning

confidence: 99%