About

Meni Wanunu is a professor at Northeastern University College of Engineering, with affiliations in the departments of Physics, Bioengineering, and Chemical Engineering. His research group investigates biomolecules at the single-molecule level, developing nanopore-based and other nanotechnology methods for probing the structure and dynamic behavior of biomolecules. His work employs optical waveguides and single-molecule enzymatic approaches for RNA sequencing, as well as engineered nanopore sensors for applications in single-molecule proteomics. Wanunu's research develops devices for studying biomolecules and biomaterials, utilizing experimental techniques complemented by advanced computational tools for big data analysis. He has contributed to the development of innovative nanopore technologies, including direct RNA sequencing using electro-optical zero-mode waveguides, single-chain nanopores for protein sequencing, and hybrid nanopore designs for high-resolution sequence mapping. Wanunu has received multiple patents related to nanopore technology and has been recognized as a top scientist worldwide, being selected among the top 2% of most-cited scientists by Stanford University. His work has significant implications for biomedical devices, bioimaging, and molecular engineering.

Research topics

• Computer Science
• Nanotechnology
• Biology
• Computational biology
• Materials science
• Machine Learning
• Artificial Intelligence
• Composite material
• Genetics
• Chemical engineering
• Biochemistry
• Optoelectronics
• Bioinformatics
• Chemistry

Selected publications

• Quad-Nanopore Array Enables High-Resolution Identification of Four Single-Stranded DNA Homopolymers

  ACS Nano · 2025-03-12 · 8 citations

  article

  The solid-state nanopore technique holds the potential to develop mechanically stable and miniaturized DNA sequencing devices. However, the limited temporal resolution due to the high electric field inside the nanopore and the lack of an effective speed control strategy have hindered the realization of sequencing. Here, we reported a quad-array (four nanopores milled with ∼30 nm interpore spacing as a detection unit) that induced a redistribution of the electric field inside and outside the nanopore array and offered high-resolution discrimination of four ssDNA homopolymer types. We demonstrated that the quad-nanopore array well resolved the translocation events of polyA25 and had a length resolution of 20 nt. The molecular dynamic simulation confirmed the slowed-down translocations and superior performance of a quad-nanopore array. We found that the nanopore array configuration induced a direct reduction of the electric field inside the nanopore as well as an increase in the electrical field outside the nanopore due to electric field crosstalk. This dual benefit not only reduced the large driving force on DNA but also facilitated molecule capture through nanopores, therefore decreasing the voltage thresholds. Finally, the successful discrimination of four ssDNA homopolymer types (polyA25, polyT25, polyC25, and polyG10) was achieved using a voltage as low as 30 mV with a translocation speed of 8 μs/nt. These findings provide insights into nanopore arrays for discriminating short single-stranded nucleotides with high resolution and demonstrate promising potential for developing DNA sequencers that utilize nanopore arrays as sensing units.

  PublisherDOI

• Direct RNA sequencing of primary human T cells reveals the impact of immortalization on mRNA pseudouridine modifications

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-10

  preprintOpen access

  Abstract Immortalized cell lines are commonly used as proxies for primary cells in human biology research. For example, Jurkat leukemic T cells fundamentally contributed to uncovering T cell signaling, activation, and immune responses. However, the immortalization process can alter key cellular properties, and researchers widely believe this process could significantly change RNA modification machinery and modification sites. In this study, we focus on pseudouridine (Ψ), one of the most abundant mRNA modifications, and compare Ψ profiles in mRNA from primary and immortalized T cells using direct RNA sequencing (DRS). Surprisingly, 87% of Ψ-sites were shared between the two cell types, primarily in transcripts encoding proteins involved in essential cellular processes, including RNA-modification regulation. Furthermore, the analysis of the 13% of sites unique to each cell type reveals that Jurkat cells contained transcripts linked to immune activation and oncogenesis, while primary T cells contained transcripts associated with calcium signaling and intracellular trafficking. We provide a list of these genes, which should be considered when using immortalized cells to study RNA modifications in immunology contexts. Most differences were driven by whether the mRNA was present or absent in the immortalized or primary cell type. Interestingly, RNA-modification enzyme expression levels were highly conserved in both cell types. This suggests that site-specific differences in Ψ levels arise from regulatory processes acting in trans rather than differences in modification enzyme levels. Significance Statement It is widely believed that RNA modification machinery and modification sites could be significantly altered in immortalized cells, yet this has never been tested. Focusing on pseudouridine (Ψ), we map Ψ in the transcriptomes of primary and immortalized human T cells. Surprisingly, most sites are conserved in the primary and immortalized T cells, with several important examples of cases with cell type specificity and should be considered on a case-by-case basis. Furthermore, we evaluated RNA-modification machinery levels in primary and immortalized T cells, finding high conservation across the cell lines. Our findings demonstrate that RNA modifications are largely conserved between primary and immortalized cells, and the edge cases can be considered individually.

  PublisherOA PDFDOI

• Pore-Based RNA Evaluation for Control of Integrity, Sequence, and Errors – Quality Control (PRECISE-QC)

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-21

  preprintOpen accessSenior authorCorresponding

  RNA is at the forefront of therapeutics and gene editing technologies. Yet, RNA synthesis remains expensive and low-yield. Consequently, most oligo manufacturers abstain from synthesizing RNA oligos longer than 60-mers. Solid-phase synthesis is the current standard production method but is often fraught with low coupling yields for canonical nucleotides and even poorer coupling for modifications. This results in high levels of byproducts such as truncations and RNA infidelity. Existing analytical methods can only provide quality control metrics such as RNA length distribution or limited composition information for short oligos. Here, we developed a standard quality control metric using Oxford Nanopore direct RNA sequencing to obtain direct insight into RNA length distribution, sequence, and presence of RNA modification sites. Our pipeline identifies error-prone regions and truncation sites that occur during synthesis. Furthermore, problematic steps in the synthesis are identified and repaired. We show that our platform can produce and assess CRISPR guide RNAs with high-fidelity and higher cleavage activity, and further, that modifications can be reliably detected. We envision that our tool will serve as an integral method for quality control pipelines that assess the integrity and accuracy of synthetic RNAs and guide the improved synthesis and yield of synthesized RNAs.

  PublisherOA PDFDOI

• Pseudouridine reprogramming in the human T-cell epitranscriptome: from primary to immortalized states

  RNA · 2025-07-09 · 1 citations

  articleOpen access

  Immortalized cell lines are commonly used as proxies for primary cells in human biology research. For example, Jurkat leukemic T cells fundamentally contributed to uncovering T-cell signaling, activation, and immune responses. However, the immortalization process can alter key cellular properties, and researchers widely believe this process could significantly change RNA modification machinery and modification sites. In this study, we focus on pseudouridine (ψ), one of the most abundant mRNA modifications, and compare ψ profiles in mRNA from primary and immortalized T cells using direct RNA sequencing (DRS). Surprisingly, 87% of ψ-sites were shared between the two cell types, primarily in transcripts encoding proteins involved in essential cellular processes, including RNA-modification regulation. Furthermore, the analysis of the 13% of sites unique to each cell type reveals that Jurkat cells contained transcripts linked to immune activation and oncogenesis, while primary T cells contained transcripts associated with calcium signaling and intracellular trafficking. We provide a list of these genes, which should be considered when using immortalized cells to study RNA modifications in immunology contexts. Most differences were driven by whether the mRNA was present or absent in the immortalized or primary cell type. Interestingly, RNA-modification enzyme expression levels were highly conserved in both cell types. This suggests that site-specific differences in ψ levels arise from regulatory processes acting in trans rather than differences in modification enzyme levels.

  PublisherOA PDFDOI

• inCu-click: DNA-enhanced ligand enables live-cell, intracellular click chemistry reaction with copper catalyst

  Nature Communications · 2025-05-23 · 6 citations

  articleOpen access

  Labeling cellular biomolecules via copper-catalyzed azide-alkyne cycloaddition (CuAAC) offers rapid reaction kinetics and uses small azide and alkyne probes that minimally disturb molecular function, making it ideal for tracking biomolecules. However, applying CuAAC inside living cells has been hindered by the high copper levels required, which compromise cell health. To overcome this barrier, here, we develop inCu-click, an intracellular CuAAC approach that employs a DNA-conjugated ligand (BTT-DNA) to localize and concentrate copper ions at the reaction site. This design permits efficient click chemistry at low intracellular copper concentrations without added copper salts and supports template-driven proximity and liposomal delivery of the ligand into cells. Here we show that inCu-click enables robust fluorescent labeling of nascent phospholipids and proteins in live cells with negligible impact on viability, establishing a platform for real-time visualization of biomolecule dynamics in complex, live cell environments.

  PublisherDOI

• Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess epitranscriptome plasticity in a neuronal cell line

  Cell Systems · 2025-03-20 · 7 citations

  articleOpen access
  PublisherOA PDFDOI

• Chemical Composition and Backbone Modifications Define Deformability of Nucleic Acid Nanoparticles

  ACS Nano · 2025-07-03 · 5 citations

  articleOpen accessSenior authorCorresponding

  Nucleic acid nanoparticles (NANPs), composed of short oligonucleotides assembled into specific architectures, are emerging as a programmable platform for the regulated drug delivery of various therapeutic agents. Here, we use a nanopore "clamp" to investigate the mechanical properties of six-stranded RNA and DNA-based NANPs with the connectivity of a cube of sizes below 10 nm. When electrophoretically forced through solid-state nanopores that are smaller than the cubes, deformation of the NANPs generates prolonged electrical signatures whose durations depend on the mechanical deformability of the structures. All-atom MD simulations further reveal differences in the mechanical flexibility of DNA, RNA, modified RNA, and hybrid DNA/RNA cubes, supporting these findings at the molecular level. While DNA cubes deform and translocate through the pore, analogous RNA cubes are too stiff and cannot squeeze through at a comparable voltage, despite having the same sequence and overall shape as the DNA cubes. Further, we find that hybrid RNA/DNA cubes exhibit intermediate mechanical deformability to pure DNA or RNA cubes, indicating an additive effect of the RNA content on nanocube stiffness. Finally, different chemical modifications introduced to the strands can be used to fine-tune the mechanical properties of the NANPs.

  PublisherDOI

• Rare bioactive diffusible tau species from Alzheimer brain support both templated misfolding and fibril formation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-25

  preprintOpen access

  The accumulation of hyperphosphorylated tau aggregates is a hallmark of Alzheimer's disease (AD). In addition to long-recognized tau deposits in neurofibrillary tangles, recent studies suggest that diffusible, aqueous soluble (High Molecular Weight, or HMW) species are also bioactive, i.e., able to seed templated misfolding. The characteristics of the diffusible misfolded proteins are largely unknown, and their relationship to classical fibrillar structures is unclear. Using sequential size exclusion and anion exchange chromatography, we fractionated the HMW tau population and identified multiple subspecies varying in retention properties. The subspecies that elute early from the size column, and are retained on the anion exchange column are seed competent, whereas the other soluble fractions are not. Biophysical analyses using super resolution, atomic force, and immunogold electron microscopy confirmed that the size and conformation of both bioactive and non-bioactive tau oligomers are similar, with dimers, trimers, and tetramers predominating. The presence of surface phosphorylations, as detected by recently developed single molecule array (SIMOA) analyses, correlates with seeding capacity. Single bioactive tau oligomers at fMol concentrations can induce seeding and templated misfolding in a reporter cell. The bioactive species can alternatively support aggregation of a truncated repeat domain tau construct into thioflavin T positive fibrils in a real-time quacking-induced conversion (RT-QuIC) assay, whereas full length recombinant tau yields oligomers. These findings provide structural insights into bioactive oligomeric tau species, emphasize the small concentrations necessary for bioactivity, and highlight the possibility that, under different conditions, they can seed either oligomeric or fibrillar structures.

  PublisherOA PDFDOI

• Author response for "Hydrophilicity and surface charge modulation of Ti<sub>3</sub>C<sub>2</sub>T<sub><i>x</i></sub> MXene based membranes for water desalination"

  2024-06-15

  peer-reviewSenior author
  PublisherDOI

• Terminal tagging of full-length proteins for enhanced capturing by biological nanopores

  Biophysical Journal · 2024-02-01 · 1 citations

  articleSenior author
  PublisherDOI

Recent grants

• Picogram-level DNA sequencing using Nanopores and Zero-Mode Waveguides

  NIH · $812k · 2012–2016

• Direct picogram DNA and RNA sequencing using nanopore Zero-mode waveguides

  NIH · $2.3M · 2019–2022

• Ion Fountain Nanopore Readers for High-Resolution DNA and RNA Sequencing

  NIH · $627k · 2021–2023

• Bilateral NSF/BIO-BBSRC: Engineering Tunable Portal Hybrid Nanopores for High-Resolution Sequence Mapping

  NSF · $500k · 2016–2020

Frequent coauthors

• Robert Y. Henley

  Northeastern University

  29 shared

• Marija Drndić

  26 shared

• Aleksei Aksimentiev

  University of Illinois Urbana-Champaign

  25 shared

• Amr Makhamreh

  Northeastern University

  21 shared

• Xinqi Kang

  Northeastern University

  20 shared

• Hirohito Yamazaki

  Nagaoka University of Technology

  20 shared

• A. Meller

  Technion – Israel Institute of Technology

  19 shared

• Mehrnaz Mojtabavi

  Northeastern University

  19 shared

Labs

• Wanunu LabPI

Education

• Ph.D., Chemistry

  Weizmann Institute of Science

  2005

Awards & honors

• 2024 Stanford University Annual Assessment of Author Citatio…
• 2025 Stanford University Annual Assessment of Author Citatio…
• Patent for Hybrid Nanopore Technology for Biomolecule Sensin…
• Patent for Single-Molecule Protein Analysis
• Northeastern NAI Innovator of the Year Award