Site-Specific Protein Photochemical Covalent Attachment to Carbon Nanotube Side Walls and Its Electronic Impact on Single Molecule Function

Ultrafast Laser Processing of 2D Materials: Novel Routes to Advanced Devices

Ultrafast laser processing has emerged as a versatile technique for modifying materials and introducing novel functionalities. Over the past decade, this method has demonstrated remarkable advantages in the manipulation of 2D layered materials, including synthesis, structuring, functionalization, and local patterning. Unlike continuous-wave and long-pulsed optical methods, ultrafast lasers offer a solution for thermal heating issues. Nonlinear interactions between ultrafast laser pulses and the atomic lattice of 2D materials substantially influence their chemical and physical properties. This paper highlights the transformative role of ultrafast laser pulses in maskless green technology, enabling subtractive, and additive processes that unveil ways for advanced devices. Utilizing the synergetic effect between the energy states within the atomic layers and ultrafast laser irradiation, it is feasible to achieve unprecedented resolutions down to several nanometers. Recent advancements are discussed in functionalization, doping, atomic reconstruction, phase transformation, and 2D and 3D micro- and nanopatterning. A forward-looking perspective on a wide array of applications of 2D materials, along with device fabrication featuring novel physical and chemical properties through direct ultrafast laser writing, is also provided.

Photo-induced protein modifications: a range of biological consequences and applications

Proteins are the most abundant biomolecules in living organisms and tissues and are also present in many natural and processed foods and beverages, as well as in pharmaceuticals and therapeutics. When exposed to UV-visible light, proteins containing endogenous or exogenous chromophores can undergo direct and indirect photochemical processes, resulting in protein modifications including oxidation of residues, cross-linking, proteolysis, covalent binding to molecules and interfaces, and conformational changes. When these modifications occur in an uncontrolled manner in a physiological context, they can lead to biological dysfunctions that ultimately result in cell death. However, rational design strategies involving light-activated protein modification have proven to be a valuable tool for the modulation of protein function or even for the construction of new biomaterials. This mini-review describes the fundamentals of photochemical processes in proteins and explores some of their emerging biomedical and nanobiotechnological applications, such as photodynamic therapy (PDT), photobonding for wound healing, photobioprinting, photoimmobilization of biosensors and enzymes for sensing, and biocatalysis, among others.

Covalent conjugation of proteins onto fluorescent single-walled carbon nanotubes for biological and medical applications

Single-walled carbon nanotubes (SWCNTs) have optical properties that are conducive for biological applications such as sensing, delivery, and imaging. These applications necessitate the immobilization of macromolecules that can serve as therapeutic drugs, molecular templates, or modulators of surface interactions. Although previous studies have focused on non-covalent immobilization strategies, recent advances have introduced covalent functional handles that can preserve or even enhance the SWCNT optical properties. This review presents an overview of covalent sidewall modifications of SWCNTs, with a focus on the latest generation of "sp³ defect" modifications. We summarize and compare the reaction conditions and the reported products of these sp³ chemistries. We further review the underlying photophysics governing SWCNT fluorescence and apply these principles to the fluorescence emitted from these covalently modified SWCNTs. Finally, we provide an outlook on additional chemistries that could be applied to covalently conjugate proteins to these chemically modified, fluorescent SWCNTs. We review the advantages of these approaches, emerging opportunities for further improvement, as well as their implications for enabling new technologies.

Fabrication and Functionalisation of Nanocarbon-Based Field-Effect Transistor Biosensors

Nanocarbon-based field-effect transistor (NC-FET) biosensors are at the forefront of future diagnostic technology. By integrating biological molecules with electrically conducting carbon-based platforms, high sensitivity real-time multiplexed sensing is possible. Combined with their small footprint, portability, ease of use, and label-free sensing mechanisms, NC-FETs are prime candidates for the rapidly expanding areas of point-of-care testing, environmental monitoring and biosensing as a whole. In this review we provide an overview of the basic operational mechanisms behind NC-FETs, synthesis and fabrication of FET devices, and developments in functionalisation strategies for biosensing applications.

One-Step Photochemical Immobilization of Aptamer on Graphene for Label-Free Detection of NT-proBNP

A novel photochemical technological route for one-step functionalization of a graphene surface with an azide-modified DNA aptamer for biomarkers is developed. The methodology is demonstrated for the functionalization of a DNA aptamer for an N-terminal B-type natriuretic peptide (NT-proBNP) heart failure biomarker on the surface of a graphene channel within a system based on a liquid-gated graphene field effect transistor (GFET). The limit of detection (LOD) of the aptamer-functionalized sensor is 0.01 pg/mL with short response time (75 s) for clinically relevant concentrations of the cardiac biomarker, which could be of relevance for point-of-care (POC) applications. The novel methodology could be applicable for the development of different graphene-based biosensors for fast, stable, real-time, and highly sensitive detection of disease markers.

Single molecule DNA origami nanoarrays with controlled protein orientation

The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.

Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices

The ability to detect proteins through gating conductance by their unique surface electrostatic signature holds great potential for improving biosensing sensitivity and precision. Two challenges are: (1) defining the electrostatic surface of the incoming ligand protein presented to the conductive surface; (2) bridging the Debye gap to generate a measurable response. Herein, we report the construction of nanoscale protein-based sensing devices designed to present proteins in defined orientations; this allowed us to control the local electrostatic surface presented within the Debye length, and thus modulate the conductance gating effect upon binding incoming protein targets. Using a β-lactamase binding protein (BLIP2) as the capture protein attached to carbon nanotube field effect transistors in different defined orientations. Device conductance had influence on binding TEM-1, an important β-lactamase involved in antimicrobial resistance (AMR). Conductance increased or decreased depending on TEM-1 presenting either negative or positive local charge patches, demonstrating that local electrostatic properties, as opposed to protein net charge, act as the key driving force for electrostatic gating. This, in turn can, improve our ability to tune the gating of electrical biosensors toward optimized detection, including for AMR as outlined herein.

Tuning Electrostatic Gating of Semiconducting Carbon Nanotubes by Controlling Protein Orientation in Biosensing Devices

The ability to detect proteins through gating conductance by their unique surface electrostatic signature holds great potential for improving biosensing sensitivity and precision. Two challenges are: (1) defining the electrostatic surface of the incoming ligand protein presented to the conductive surface; (2) bridging the Debye gap to generate a measurable response. Herein, we report the construction of nanoscale protein-based sensing devices designed to present proteins in defined orientations; this allowed us to control the local electrostatic surface presented within the Debye length, and thus modulate the conductance gating effect upon binding incoming protein targets. Using a β-lactamase binding protein (BLIP2) as the capture protein attached to carbon nanotube field effect transistors in different defined orientations. Device conductance had influence on binding TEM-1, an important β-lactamase involved in antimicrobial resistance (AMR). Conductance increased or decreased depending on TEM-1 presenting either negative or positive local charge patches, demonstrating that local electrostatic properties, as opposed to protein net charge, act as the key driving force for electrostatic gating. This, in turn can, improve our ability to tune the gating of electrical biosensors toward optimized detection, including for AMR as outlined herein.

Designed Artificial Protein Heterodimers With Coupled Functions Constructed Using Bio-Orthogonal Chemistry

The formation of protein complexes is central to biology, with oligomeric proteins more prevalent than monomers. The coupling of functionally and even structurally distinct protein units can lead to new functional properties not accessible by monomeric proteins alone. While such complexes are driven by evolutionally needs in biology, the ability to link normally functionally and structurally disparate proteins can lead to new emergent properties for use in synthetic biology and the nanosciences. Here we demonstrate how two disparate proteins, the haem binding helical bundle protein cytochrome b 562 and the β-barrel green fluorescent protein can be combined to form a heterodimer linked together by an unnatural triazole linkage. The complex was designed using computational docking approaches to predict compatible interfaces between the two proteins. Models of the complexes where then used to engineer residue coupling sites in each protein to link them together. Genetic code expansion was used to incorporate azide chemistry in cytochrome b 562 and alkyne chemistry in GFP so that a permanent triazole covalent linkage can be made between the two proteins. Two linkage sites with respect to GFP were sampled. Spectral analysis of the new heterodimer revealed that haem binding and fluorescent protein chromophore properties were retained. Functional coupling was confirmed through changes in GFP absorbance and fluorescence, with linkage site determining the extent of communication between the two proteins. We have thus shown here that is possible to design and build heterodimeric proteins that couple structurally and functionally disparate proteins to form a new complex with new functional properties.

DNA-Directed Assembly of Carbon Nanotube-Protein Hybrids

Here, we report the controlled assembly of SWCNT–GFP hybrids employing DNA as a linker. Two distinct, enriched SWCNTs chiralities, (6,5), (7,6), and an unsorted SWCNT solution, were selectively functionalized with DNA and hybridized to a complementary GFP^DNA conjugate. Atomic force microscopy images confirmed that GFP attachment occurred predominantly at the terminal ends of the nanotubes, as designed. The electronic coupling of the proteins to the nanotubes was confirmed via in-solution fluorescence spectroscopy, that revealed an increase in the emission intensity of GFP when linked to the CNTs.

Single molecule electronic devices with carbon-based materials: status and opportunity

The field of single molecule electronics has progressed remarkably in the past decades by allowing for more versatile molecular functions and improving device fabrication techniques. In particular, electrodes made from carbon-based materials such as graphene and carbon nanotubes (CNTs) may enable parallel fabrication of multiple single molecule devices. In this perspective, we review the recent progress in the field of single molecule electronics, with a focus on devices that utilizes carbon-based electrodes. The paper is structured in three main sections: (i) controlling the molecule/graphene electrode interface using covalent and non-covalent approaches, (ii) using CNTs as electrodes for fabricating single molecule devices, and (iii) a discussion of possible future directions employing new or emerging 2D materials.