The role of a diamondoid as a hydrogen donor or acceptor in probing DNA nucleobases

Maier, Frank; Sivaraman, Ganesh; Fyta, Maria

doi:10.1140/epje/i2014-14095-0

Cited by 9 publications

(6 citation statements)

References 34 publications

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“…Clearly distinct and nucleotide specific peaks are revealed denoting that the nucleotides can be distinguished from each other through these peaks. These are related to the specific hydrogen bonding of the diamondoid and the nucleotide . Our results show, that the transmission peaks for all rotations can be associated to peaks in the local electronic density of states (not shown) for all nucleotides.…”

Section: Resultsmentioning

confidence: 60%

“…These have tunable optoelectronic properties, are thermodynamically very stable, vary in size and can be selectively modified . Derivatives of diamondoids, can be double modified in order to graft on the gold surface on one side, while on the other side these offer donor/acceptor sites for hydrogen binding to DNA nucleotides . We have already shown that such a device shows a high DNA selectivity also in the presence of a water solvent …”

Section: Introductionmentioning

confidence: 99%

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Functionalized Nanogap for DNA Read‐Out: Nucleotide Rotation and Current‐Voltage Curves

Maier

Fyta

2020

ChemPhysChem

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Functionalized nanogaps embedded in nanopores show a strong potential for enhancing the detection of biomolecules, their length, type, and sequence. This detection is strongly dependent on the features of the target biomolecules, as well as the characteristics of the sensing device. In this work, through quantum‐mechanical calculations, we elaborate on representative such aspects for the specific case of DNA detection and read‐out. These aspects include the influence of single DNA nucleotide rotation within the nanogap and the current‐voltage (I‐V) characteristics of the nanogap. The results unveil a distinct variation in the electronic current across the functionalized device for the four natural DNA nucleotides with the applied voltage. These also underline the asymmetric response of the rotating nucleotides on this applied voltage and the respective variation in the rectification ratio of the device. The electronic tunneling current across the nanogap can be further enhanced through the proper choice of an applied bias voltage. We were able to correlate the enhancement of this current to the nucleotide rotation dynamics and a shift of the electronic transmission peaks towards the Fermi level. This nucleotide specific shift further reveals the sensitivity of the device in reading‐out the identity of the DNA nucleotides for all different configurations in the nanogap. We underline the important information that can be obtained from both the I‐V curves and the rectification characteristics of the nanogap device in view of accurately reading‐out the DNA information. We show that tuning the applied bias can enhance this detection and discuss the implications in view of novel functionalized nanopore sequencers.

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Section: Resultsmentioning

confidence: 60%

Section: Introductionmentioning

confidence: 99%

Functionalized Nanogap for DNA Read‐Out: Nucleotide Rotation and Current‐Voltage Curves

Maier

Fyta

2020

ChemPhysChem

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“…In addition, it was found that the size of the diamondoids can affect the melting temperature of the DNA [161]. These findings have initiated a number of theoretical studies [162][163][164][165][166][167][168][169] on exploring the possibility of using diamondoid-based 3D nanoarchitectures in the field of bionanotechnology [170], such as new biosensors with high sensitivity [162].…”

Section: Biological and Medical Applicationsmentioning

confidence: 99%

Nanotechnology of diamondoids for the fabrication of nanostructured systems

Yeung

Dong

Chen

et al. 2020

Nanotechnology Reviews

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Diamondoids are cage-like hydrocarbon materials with unique characteristics such as low dielectric constants, negative electron affinity, large steric bulk, and electron-donating ability. They are widely used for advanced functional materials in nanocomposite science. Surface modification of diamondoids also produces functional derivatives that broaden its applications. This article provides a concise review of the fundamentals of diamondoids, including their origin and functionalization, electronic structure, optical properties, and vibrational characteristics. The recent advances of diamondoids and their derivatives in applications, such as nanocomposites and thin film coatings, are presented. The fabrication of diamondoid-based nanostructured devices, including electron emitters, catalyst sensors, and light-emitting diodes, are also reviewed. Finally, the future developments of this unique class of hydrocarbon materials in producing a novel nanostructure system using advanced nanotechnologies are discussed. This review is intended to provide a basic understanding of diamondoid properties, discuss the recent progress of its modifications and functionalization, and highlight its novel applications and future prospects.

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“…[88][89][90][91] When the diamondoids bind with a DNA unit (such as nucleobase), the electronic band gaps will be significantly affected even with weak interaction energies. [88][89][90][91] When the diamondoids bind with a DNA unit (such as nucleobase), the electronic band gaps will be significantly affected even with weak interaction energies.…”

Section: Diamondoids In Pharmaceuticalsmentioning

confidence: 99%

“…Very recently, diamondoids and their derivatives were explored as probes and biosensors for DNA due to the strong hydrogen bonds between the diamondoids and DNA units. [88][89][90][91] When the diamondoids bind with a DNA unit (such as nucleobase), the electronic band gaps will be significantly affected even with weak interaction energies. As such, diamondoids can clearly distinguish the regular nucleobase from the modified nucleobase.…”

Section: Diamondoids In Pharmaceuticalsmentioning

confidence: 99%

Derivatization of diamondoids for functional applications

et al. 2015

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Diamondoids, a group of hydrocarbon cage molecules that resemble diamond lattice, are attracting increasing interest in the past decade. Their diamond-like structure warrants that diamondoids inherit the superior properties of diamond at nanoscale, including exceptional hardness and stiffness, high thermal stability, high chemical resistance, unique optical properties and fluorescence, and excellent biocompatibility. To effectively take advantage of the fascinating properties of diamondoids, they must be properly functionalized so that they can be covalently incorporated into the host systems or compatibly mixed with the hosts. Herein, the origin, synthesis, derivatization, and application of diamondoids are reviewed. In particular, how the derivatized diamondoids for various functional applications, including pharmaceuticals, polymers, fine chemicals, nanomaterials, and optical devices, are discussed. It is hoped that this review article can attract more interest in diamondoids, which in turn helps motivate the development of new synthesis and application of diamondoids and their derivatives so that this group of unique molecules can bring more benefits. Scheme 3 Bromination of adamantane under phase-transfer conditions.Scheme 4 Synthesis of 1,3,5,7-tetrabromoadamantane.Scheme 5 Preparation of 1-adamantanol by the ozonation of adamantane over silica gel.Scheme 6 Preparation of adamantyl amine.Scheme 7 Preparation of 1,3-adamantanedicarboxylic acid.

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The role of a diamondoid as a hydrogen donor or acceptor in probing DNA nucleobases

Cited by 9 publications

References 34 publications

Functionalized Nanogap for DNA Read‐Out: Nucleotide Rotation and Current‐Voltage Curves

Functionalized Nanogap for DNA Read‐Out: Nucleotide Rotation and Current‐Voltage Curves

Nanotechnology of diamondoids for the fabrication of nanostructured systems

Derivatization of diamondoids for functional applications

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