Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides

Sivaraman, Ganesh; Amorim, Rodrigo G.; Scheicher, Ralph H.; Fyta, Maria

doi:10.1039/c6nr00500d

Cited by 34 publications

(42 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The bias voltage we have applied ranges from −1 V to +1 V in steps of 0.1 V. Note, that no solvent is present and a bias of ±1 V cannot dissociate water in our model. Further details on the theory and its numerical implementation can be found elsewhere …”

Section: Methodsmentioning

confidence: 99%

“…These factors hinder an error‐free, rapid, and low‐cost DNA sequencing through solid‐state nanopores. In order to enhance the signal‐to‐noise ratio, we have previously proposed the use of a tiny modified nanodiamond particle to functionalize the gold electrodes in a nanopore . This small particle is the smallest of a family known as diamondoids, which are nanoscale diamond‐like carbon nanocages terminated by hydrogen atoms .…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Maier

Fyta

2020

ChemPhysChem

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Maier

Fyta

2020

ChemPhysChem

Self Cite

View full text Add to dashboard Cite

show abstract

“…We have used the generalized gradient approximation of Perdew-Burke-Erzernhof (PBE-GGA) [56], and the norm-conserving Troullier-Martins pseudopotentials [57]. For the basis set, we have considered a double-ζ with polarization basis-set (DZP) for the molecules, and a single-ζ with polarization (SZP) for the gold atoms (5d , 6S 10 1 ) which has been proven efficient for similar setup [58]. An energy shift of 0.01 Ry with a real space sampling grid (mesh cutoff) of 200 Ry.…”

Section: Methodsmentioning

confidence: 99%

Diamondoid-based molecular junctions: a computational study

Adhikari

Sivaraman²,

Fyta³

2016

Nanotechnology

Self Cite

View full text Add to dashboard Cite

In this work, we deal with the computational investigation of diamondoid-based molecular conductance junctions and their electronic transport properties. A small diamondoid is placed between the two gold electrodes of the nanogap and is covalently bonded to the gold electrodes through two different molecules, a thiol group and a N-heterocyclic carbene molecule. We have shown that the thiol linker is more efficient as it introduces additional electron paths for transport at lower energies. The influence of doping the diamondoid on the properties of the molecular junctions has been investigated. We find that using a nitrogen atom to dope the diamondoids leads to a considerable increase of the zero bias conductance. For the N-doped system we show an asymmetric feature of the I-V curve of the junctions resulting in rectification within a very small range of bias voltages. The rectifying nature is the result of the characteristic shift in the bias-dependent highest occupied molecular orbital state. In all cases, the efficiency of the device is manifested and is discussed in view of novel nanotechnological applications.

show abstract

“…In principle, fully sequencing of the whole genome would provide all the information required for such an endeavor. Nonetheless, that is still a cumbersome, slow and expensive process [5,6,7,8], even though there are proposals for next-generation single-shot sequencing [9,10,11].…”

Section: Introductionmentioning

confidence: 99%

Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates

2019

View full text Add to dashboard Cite

In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green’s functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.

show abstract

Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides

Cited by 34 publications

References 36 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

Diamondoid-based molecular junctions: a computational study

Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates

Contact Info

Product

Resources

About