Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/<i>h</i>-BN nanopore

Souza, Fábio A. L. de; Sivaraman, Ganesh; Fyta, Maria; Scheicher, Ralph H.; Scopel, Wanderlã L.; Amorim, Rodrigo G.

doi:10.1039/d0nr04363j

Cited by 28 publications

(40 citation statements)

References 46 publications

(55 reference statements)

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“…The interaction with the pore edges predominantly dominates the residual or dwelling time of each target nucleotide. However, the drag force of the adjacent nucleotide plays a significant role in the speed of the translocation process . All the E i values for graphene and χ3 borophene pores are higher than the thermal energy at room temperature (0.026 eV), suggesting that higher temperature may not affect the geometrical configuration of targeted nucleotide when translocated through the pores.…”

Section: Resultsmentioning

confidence: 94%

“…From Figure , we observed that electronegative atoms (N and O atoms) of nucleotides are at a length less than 2.8 Å, which is considered to exhibit H-bonding . From the interaction energy ( E i ) values, ranges that are in the range of 0.40–0.45 eV/H-bond indicate that the interactions are H-bonding types of interactions . The reason behind the different interaction energy range for both the devices could be the chemistry of their pore edges.…”

Section: Resultsmentioning

confidence: 98%

“…The shift in the transmission resonance peak can be assigned to the optimum electrostatic interaction of the polar (C δ− –H δ+ ) bond at pore edges with the negatively charged sites of the targeted nucleotide. In addition, the induced dipole-moment on the partially charged sites of the nucleotides near the locality of the nanopore causes the charge redistribution (Figure a), which generates a change in electric potential around the C chains of nanopore edges . The G 0 spectra of dGMP are found to be distinctively high compared to the other three nucleotides in the positive energy region (0 to 0.6 eV).…”

Section: Resultsmentioning

confidence: 99%

“…In addition, the induced dipole-moment on the partially charged sites of the nucleotides near the locality of the nanopore causes the charge redistribution (Figure 4a), which generates a change in electric potential around the C chains of nanopore edges. 57 The G 0 spectra of dGMP are found to be distinctively high compared to the other three nucleotides in the positive energy region (0 to 0.6 eV). At the same time, it is lower in the negative energy region (0 to −0.5 eV).…”

Section: Model and Computational Detailsmentioning

confidence: 94%

“…56 From the interaction energy (E i ) values, ranges that are in the range of 0.40−0.45 eV/H-bond indicate that the interactions are H-bonding types of interactions. 57 The reason behind the different interaction energy range for both the devices could be the chemistry of their pore edges. In graphene (C δ− −H δ+ ) and χ3 borophene (B δ+ −H δ− ) pore edges, the H atoms partially act as protons (H δ+ ) and hydrides (H δ− ), respectively.…”

Section: Model and Computational Detailsmentioning

confidence: 99%

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First-Principles Density Functional Theory Study on Graphene and Borophene Nanopores for Individual Identification of DNA Nucleotides

Jena

Kumawat

Pathak

2021

ACS Appl. Nano Mater.

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The advancement in DNA sequencing has massively improved the biological and medicinal research, leading to the development of new medical diagnosis and forensic applications. It puts forward a pool of information that could be harnessed to realize personalized medicine toward various deadly diseases. Recent developments in solid-state nanopore-based sequencing technology have drawn much attention owing to its potential to achieve fast, cost-effective, reliable, and single-shot nucleotide identification. Here, we have proposed atomically thin graphene and χ3 borophene nanopore-based devices for DNA sequencing. The structural and electronic properties of the graphene pore and χ3 borophene pore with and without DNA nucleotides have been studied by employing first-principles density functional theory (DFT) calculations. Using the DFT and non-equilibrium Green’s function formalism (NEGF), we have studied the transverse conductance and current–voltage (I–V) characteristics of all the systems. We have observed that nucleotides are weakly interacting with the χ3 borophene pore compared with the graphene pore, indicating higher translocation speed and shorter residence time inside the χ3 borophene pore. In case of both the nanopores, the operating current across the devices is within the range of microampere (μA), which is several orders higher magnitude than that of the previously reported nanogap/nanopore-based devices. The I–V results show that the graphene nanopore-based device is promising for individual identification of nucleotides compared to the χ3 borophene pore-based device, and the results are promising compared to even the graphene nanogap-based systems reported earlier.

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Section: Resultsmentioning

confidence: 94%

Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Section: Model and Computational Detailsmentioning

confidence: 94%

Section: Model and Computational Detailsmentioning

confidence: 99%

See 3 more Smart Citations

First-Principles Density Functional Theory Study on Graphene and Borophene Nanopores for Individual Identification of DNA Nucleotides

Jena

Kumawat

Pathak

2021

ACS Appl. Nano Mater.

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Protein Sequencing with Artificial Intelligence: Machine Learning Integrated Phosphorene Nanoslit

Mittal,

Jena,

Pathak

2023

Chemistry A European J

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Achieving high throughput protein sequencing at single molecule resolution remains a daunting challenge. Herein, relying on a solid‐state 2D phosphorene nanoslit device, we report an extraordinary biosensor to rapidly identify the key signatures of all twenty amino acids using interpretable machine learning (ML) model. The XGBoost regression algorithm allows the determination of transmission function of all twenty amino acids with high accuracy. The resultant ML and DFT studies reveal that it is possible to identify individual amino acids through transmission and current signals readouts with high sensitivity and selectivity. Moreover, we thoroughly compared our results to those from graphene nanoslit and found that the phosphorene nanoslit device can be an ideal candidate for protein sequencing up to a 13‐fold increase in transmission sensitivity. The present study facilitates high throughput screening of all twenty amino acids and can be further extended to other biomolecules for disease diagnosis and therapeutic decision‐making.

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Structural Properties of Hachimoji Nucleic Acids and Their Building Blocks: Comparison of Genetic Systems with Four, Six and Eight Alphabets

et al. 2022

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Expansion of the genetic alphabet is an ambitious goal. A recent breakthrough has led to the eight-base (hachimoji) genetics having canonical and unnatural bases. However, very little is known on the molecular-level features that facilitate the candidature of unnatural bases as genetic alphabets. Here we amalgamated DFT calculations and MD simulations to analyse the properties of the constituents of hachimoji DNA and RNA. DFT reveals the dominant syn conformation for isolated unnatural deoxyribonucleosides and at the 5'-end of oligonucleotides, although an anti/syn mixture is predicted at the nonterminal and 3'-terminal positions. However, isolated ribonucleotides prefer an anti/syn mixture, but mostly prefer anti conformation at the nonterminal positions. Further, the canon-ical base pairing combinations reveals significant strength, which may facilitate replication of hachimoji DNA. We also identify noncanonical base pairs that can better tolerate the substitution of unnatural pairs in RNA. Stacking strengths of 51 dimers reveals higher average stacking stabilization of dimers of hachimoji bases than canonical bases, which provides clues for choosing energetically stable sequences. A total of 14.4 μs MD simulations reveal the influence of solvent on the properties of hachimoji oligonucleotides and point to the likely fidelity of replication of hachimoji DNA. Our results pinpoint the features that explain the experimentally observed stability of hachimoji DNA.

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Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/h-BN nanopore

Abstract: The feasibility of synthesizing unnatural DNA/RNA has recently been demonstrated, giving rise to new perspectives and challenges in the emerging field of synthetic biology, DNA data storage, and even the...

Cited by 28 publications

References 46 publications

First-Principles Density Functional Theory Study on Graphene and Borophene Nanopores for Individual Identification of DNA Nucleotides

First-Principles Density Functional Theory Study on Graphene and Borophene Nanopores for Individual Identification of DNA Nucleotides

Protein Sequencing with Artificial Intelligence: Machine Learning Integrated Phosphorene Nanoslit

Structural Properties of Hachimoji Nucleic Acids and Their Building Blocks: Comparison of Genetic Systems with Four, Six and Eight Alphabets

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