Effect of single nanoparticle-nanopore interaction strength on ionic current modulation

https://doi.org/10.1016/j.snb.2020.128785Get rights and content

Highlights

  • Debye layer interactions cause bi-directional current profile in conical pore.

  • Dwell time of the target analyte exhibits extreme sensitivity to the interaction strength between target and nanopore.

  • Sign of current modulation depends on the strength of nanoparticle-pore interactions.

  • Poly-electrolyte functionalization is used to modify electrostatic force of interaction between nanoparticle and nanopore.

Abstract

Solid-state nanopores are rapidly emerging as promising platforms for developing various single molecule sensing applications. The modulation of ionic current through the pore due to translocation of the target molecule has been the dominant measurement modality in nanopore sensors. Here, we focus on the dwell time, which is the duration taken by the target molecule or particle to traverse the pore and study its dependence on the strength of interaction of the target with the pore using single gold nanoparticles (NPs) as targets interacting with a silicon nitride (SiN) nanopore. The strength of interaction, which in our case is electrostatic in nature, can be controlled by coating the nanoparticles with charged polymers. We report on an operating regime of this nanopore sensor, characterized by attractive interactions between the nanoparticle and the pore, where the dwell time is exponentially sensitive to the target-pore interaction. We used negatively and positively charged gold nanoparticles to control the strength of their interaction with the Silicon Nitride pore which is negatively charged. Our experiments revealed how this modulation of the electrostatic force greatly affects the dwell time. Positively charged NPs with strong attractive interactions with the pore resulted in increase of dwell times by 2–3 orders of magnitude, from 0.4 ms to 75.3 ms. This extreme sensitivity of the dwell time on the strength of interaction between a target and nanopore can be exploited in emerging nanopore sensor applications.

Introduction

The nanopore measurement technique has gained prominence due to its potential in label-free high-throughput single-molecule detection [[1], [2], [3], [4], [5], [6], [7]]. The concept is simple; a single nanometer sized pore forms the only means of passage through an otherwise impermeable membrane between the two chambers of a fluidic cell. On applying an electrical potential difference between the two chambers, the molecule or target analyte of interest is driven through the pore and subsequently modulates the ionic current based on its conformation and charge distribution. Nanopores with a comparable dimension as that of the analyte gives a detectable current signature every time there is a passage of the molecule [[8], [9], [10]]. Recent advances in fabrication methods have made solid-state nanopores a popular choice. The solid-state nanopores are mechanically robust compared to biological nanopores [11] and have the added advantage of scalable manufacturing based on conventional silicon chip fabrication methods [[12], [13], [14], [15], [16]].

Nanopore detection technique, as opposed to bulk detection techniques such as sample conductance measurement, does not involve ensemble averaging. Nanopore devices enable us to detect analytes at the single molecule resolution which has produced many new physical insights. As the molecule passes through the nanopore it produces a characteristic current profile. These current signatures generally contain two kinds of information. First, the amplitude of current modulation due to a translocation event and second, the duration of the current modulation, which in this article we refer to as the dwell time of the target analyte through the nanopore. By using 5 nm and 10 nm diameter gold nanoparticles (NP) and by modifying their surfaces to enable strong, attractive electrostatic interactions with the nanopore walls, we investigate how the difference in their size, surface charge (and consequently NP-nanopore interaction) affect these two types of information in the ionic current traces. In particular, the exponential dependence of escape rate from an attractive trap [19,20], leads to large differences in dwell time depending on the strength of interaction, which controls the trap depth. In other words, the dwell time of the target inside the nanopore is exponentially dependent on the strength of the interaction between the target and the nanopore. This means that minor difference in the interaction strength, for example single base mismatches between single stranded DNA immobilized on translocating NP and the nanopore, can result in measurable differences in the dwell time. In this manner highly sensitive dwell time based nanopore sensors could be developed for various applications.

Although intuitively we imagine that the translocation of an NP through the nanopore would cause a reduction in current from its baseline, due to the blocking of the pore by the NP, under certain conditions it is known that an enhancement of current from the baseline value can also arise [[21], [22], [23]]. This enhancement is due to the enhanced Debye layer interactions in low ionic strength solutions. As a result, the NP carries a large charge cloud along with it which will counteract the pore blockade and result in a higher local charge density when the NP is inside the pore leading to current enhancement due to NP translocation [21,24]. We expect that the magnitude of this current enhancement effect will be directly related to the rate at which the charges are transported across the nanopore. Hence faster transport of the same magnitude of charges will result in a greater current enhancement and conversely, slower transport of charges, associated with larger dwell time values, will lead to a suppression of this enhancement effect. Indeed, we show here that the current modulation observed in our experiments can switch from an enhancement-dominated mode to a blockage-dominated mode by increasing the attractive interaction between the AuNP and the nanopore resulting in long dwell times. Thus, the dwell time and its effect on the current modulation can be used as a sensitive probe for the strength of interaction between the target analyte and the nanopore. In the subsequent sections, we present our experimental system and discuss the results in detail.

Section snippets

Nanopore fabrication

The nanopore devices were fabricated using e-beam lithography (EBL) and reactive ion etching (RIE). The process is briefly described here. Chips containing 30 um square SiN membranes of thickness 100 nm were first fabricated using low pressure chemical vapour deposition (LPCVD) of low-stress SiN followed by selective Si etch using potassium hydroxide (KOH) solution. Then an approximately 80 nm thick e-beam resist poly(methyl methacrylate) (PMMA) C3 950 K was spin-coated on top of the membrane.

Nanopore characterization

Combined analysis based on SEM, AFM and I–V characteristics revealed that the fabricated nanopores had diameters ranging from 26 nm to 32 nm [see Supplementary Information Fig. SI-1.2] and most importantly, they had a conical profile. The conical profile was evident from the AFM scans shown in Fig. 1(b) which shows conical pores with a base diameter of around 30 nm tapering down to 15−20 nm. I–V characteristics have been used to determine the diameter of nanopores. This is based on comparison

Conclusions

To summarize, Debye layer interactions combined with non-uniform pore diameter results in a bi-directional current profile, a unique feature of conical nanopore which, to the best of our knowledge has not been reported before. Utilizing the sensitivity of the conical pore we were able to differentiate two populations in a mixture of 5 nm and 10 nm nanoparticles. Moreover, we have used a method of poly-electrolyte functionalization of gold nanoparticles to modify the electrostatic force of

CRediT authorship contribution statement

Sohini Pal: Methodology, Software, Formal analysis, Investigation, Validation, Writing - original draft, Writing - review & editing, Visualization. Ramkumar B.: Resources. Sanket Jugade: Investigation. Anjana Rao: Writing - review & editing. Akshay Naik: Writing - review & editing. Banani Chakraborty: Writing - review & editing. Manoj M. Varma: Conceptualization, Supervision, Project administration, Writing - review & editing.

Declaration of Competing Interest

The authors report no declarations of interest.

Acknowledgments

The authors acknowledge the technical support provided by staff at National Nano Fabrication Facility (NNFC), Micro and Nano Characterization Facility (MNCF) at the Centre for Nano Science and Engineering (CeNSE), Indian Institute of Science, Bangalore, India. S.P. and R.K. thank Ministry of Human Resource Development (MHRD), Government of India, for research fellowship.

Sohini Pal joined the Centre for Nano Science and Engineering Department, IISc in 2015 for Ph.D. under Prof. Manoj Varma. She completed B.Tech in 2014 on Electronics and Communication Engineering (ECE) from West Bengal University of Technology, Kolkata. Her PhD research area is on Nanopore based single molecule detection.

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      Currently, nanopores are fabricated in organic and inorganic materials such as glass, 2D sheets, and polymer films. Nanopores have been fabricated on various materials such as BN (Liu et al., 2013), HfO2 (Larkin et al., 2013), MoS2 (Liu et al., 2014a), Graphene (Goyal et al., 2016; Wang et al., 2018) TiO2, SiNx (Pal et al., 2020), MXene (Mojtabavi et al., 2019), Tungsten disulfide (Danda et al., 2017), and Al2O3 (Venkatesan et al., 2010). Several companies such as Ontera (Ontera.bio, 2022), Oxford Nanopore (Oxford Nanopore Technologies, 2022), Northern Nanopore Instruments (Northern Nanopore Instruments, 2022), Nooma Bio (Home – Nooma Bio, 2022), INanobio (Home – INanoBio Inc, 2022), and Quantapore (Quantapore, 2022) have started commercializing nanopore-based technologies for sequencing and other applications.

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    Sohini Pal joined the Centre for Nano Science and Engineering Department, IISc in 2015 for Ph.D. under Prof. Manoj Varma. She completed B.Tech in 2014 on Electronics and Communication Engineering (ECE) from West Bengal University of Technology, Kolkata. Her PhD research area is on Nanopore based single molecule detection.

    Ramkumar B. obtained his B.Tech in Electrical engineering from Government College of Technology, Coimbatore, under Anna University, Chennai. He joined Dr. Varma’s group in July 2015. His current research interests are focused on nanopore based DNA sequencing and Atomistic modelling & simulation of DNA origami.

    Sanket Jugade completed his B.Tech in Mechanical Engineering from National Institute of Technology, Surathkal in 2018. He joined the Prof. Naik’s group as a Project Assistant. He is currently working on indentation experiments on suspended 2D materials using Atomic Force Microscopy.

    Dr. Anjana Rao A member of the National Academy of Sciences, Dr. Rao received her undergraduate and master’s degrees from Osmania University in India and her Ph.D. from Harvard University. After many years as a faculty member at the Harvard Medical School and the Immune Disease Institute in Boston, she joined the La Jolla Institute in 2010. She has worked on signaling and gene transcription for many years, is a member of numerous advisory panels, and has received several major awards.

    Dr. Akshay Naik received his Ph.D. in Electrical Engineering from University of Maryland, College Park, in 2006. He then worked at Caltech first as Postdoctoral Associate from 2006 to 2008 and then as Research Engineer from 2008 to 2011. In Dec 2011, he joined the Indian Institute of Science, Bangalore where he is currently an Associate Professor at the Centre for Nano Science and Engineering. His research interests are physics and application of Nano-mechanical systems.

    Dr. Banani Chakraborty received her Bachelors’ in Science degree from Presidency College, Kolkata, India in 2000 and Masters’ degree from Indian Institute of Tech- nology, Kanpur, India in 2002 in Chemistry. She has received her Doctorate (PhD in Bio-molecular Chemistry) from New York University, New York, USA in 2008 on DNA Nanotechnology. She did post-doctoral research in two stretches, first one focused on DNA aptamer-based biosensors in Simon Fraser University, British Columbia, Canada and second one as an Alexander Von Humboldt post-doctoral fellow in RWTH Aachen University, Germany where she started to functionalize DNA origami with enzymes. In 2015she joined as a Ramalingaswami Fellow (DBT) in Department of Chemical Engineering, Indian Institute of Science, Bangalore, India. Her current research focuses on functional aspect of DNA origami combining DNA aptamer-based biosensors.

    Dr. Manoj Varma received the B. tech degree from Indian Institute of Technology Madras, India, in 1999, and the Ph.D. degree from Purdue University, West Lafayette, IN, USA, in 2005. He was the Director of engineering from Quadraspec Inc., Purdue Research Foundation, from 2005 to 2007. He is currently an Associate Professor with the Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore, India. His current research interests include developing technologies for biological applications. Examples include optical techniques for biomolecular sensing, tools for cell micropatterning, integrated Lab-on-Chip devices.

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