Restriction Enzyme Analysis of Double-Stranded DNA on Pristine Single-Walled Carbon Nanotubes

Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and patterns are identified that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulations validate the stability of ssDNA conformations on SWCNTs and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, it is demonstrated that machine learning could accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for stable and sensitive molecular detection across diverse scientific disciplines.

Polymeric integration of structure-switching aptamers on transistors for histamine sensing

Aptamers that undergo large conformational rearrangements at the surface of electrolyte-gated field-effect transistor (EG-FETs)-based biosensors can overcome the Debye length limitation in physiological high ionic strength environments. For the sensitive detection of small molecules, carbon nanotubes (CNTs) that approach the dimensions of analytes of interest are promising channel materials for EG-FETs. However, functionalization of CNTs with bioreceptors using frequently reported surface modification strategies (e.g., π-π stacking), requires highly pristine CNTs deposited through methods that are incompatible with low-cost fabrication methods and flexible substrates. In this work, we explore alternative non-covalent surface chemistry to functionalize CNTs with aptamers. We harnessed the adhesive properties of poly-D-lysine (PDL), to coat the surface of CNTs and then grafted histamine-specific DNA aptamers electrostatically in close proximity to the CNT semiconducting channel. The layer-by-layer assembly was monitored by complementary techniques such as X-ray photoelectron spectroscopy, optical waveguide lightmode spectroscopy, and fluorescence microscopy. Surface characterization confirmed histamine aptamer integration into PDL-coated CNTs and revealed ∼5-fold higher aptamer surface coverage when using CNT networks with high surface areas. Specific aptamers assembled on EG-CNTFETs enabled histamine detection in undiluted high ionic strength solutions in the concentration range of 10 nM to 100 μM. Sequence specificity was demonstrated via parallel measurements with control EG-CNTFETs functionalized with scrambled DNA. Histamine aptamer-modified EG-CNTFETs showed high selectivity vs. histidine, the closest structural analog and precursor to histamine. Taken together, these results implied that target-specific aptamer conformational changes on CNTs facilitate signal transduction, which was corroborated by circular dichroism spectroscopy. Our work suggests that layer-by-layer polymer chemistry enables integration of structure-switching aptamers into flexible EG-CNTFETs for small-molecule biosensing.

Goharshadi E, Boghossian AA. Micropreparative Gel Electrophoresis for Purification of Nanoscale Bioconjugates

Conventional techniques for purifying macromolecular conjugates often require complex and costly installments that are inaccessible to most laboratories. In this work, we develop a one-step micropreparative method based on a trilayered polyacrylamide gel electrophoresis (MP-PAGE) setup to purify biological samples, synthetic nanoparticles, as well as biohybrid complexes. We apply this method to recover DNA from a ladder mixture with yields of up to 90%, compared to the 58% yield obtained using the conventional crush-and-soak method. MP-PAGE was also able to isolate enhanced yellow fluorescence protein (EYFP) from crude cell extract with 90% purity, which is comparable to purities achieved through a more complex two-step purification procedure involving size exclusion and immobilized metal-ion affinity chromatography. This technique was further extended to demonstrate size-dependent separation of a commercial mixture of graphene quantum dots (GQDs) into three different fractions with distinct optical properties. Finally, MP-PAGE was used to isolate DNA-EYFP and DNA-GQD bioconjugates from their reaction mixture of DNA and EYFP and GQD precursors, samples that otherwise could not be effectively purified by conventional chromatography. MP-PAGE thus offers a rapid and versatile means of purifying biological and synthetic nanomaterials without the need for specialized equipment.

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.

Carbon nanotube uptake in cyanobacteria for near-infrared imaging and enhanced bioelectricity generation in living photovoltaics

The distinctive properties of single-walled carbon nanotubes (SWCNTs) have inspired the development of many novel applications in the field of cell nanobiotechnology. However, studies thus far have not explored the effect of SWCNT functionalization on transport across the cell walls of prokaryotes. We explore the uptake of SWCNTs in Gram-negative cyanobacteria and demonstrate a passive length-dependent and selective internalization of SWCNTs decorated with positively charged biomolecules. We show that lysozyme-coated SWCNTs spontaneously penetrate the cell walls of a unicellular strain and a multicellular strain. A custom-built spinning-disc confocal microscope was used to image the distinct near-infrared SWCNT fluorescence within the autofluorescent cells, revealing a highly inhomogeneous distribution of SWCNTs. Real-time near-infrared monitoring of cell growth and division reveal that the SWCNTs are inherited by daughter cells. Moreover, these nanobionic living cells retained photosynthetic activity and showed an improved photo-exoelectrogenicity when incorporated into bioelectrochemical devices.

Templating colloidal sieves for tuning nanotube surface interactions and optical sensor responses

Surfactants offer a tunable approach for modulating the exposed surface area of a nanoparticle. They further present a scalable and cost-effective means for suspending single-walled carbon nanotubes (SWCNTs), which have demonstrated practical use as fluorescence sensors. Though surfactant suspensions show record quantum yields for SWCNTs in aqueous solutions, they lack the selectivity that is vital for optical sensing. We present a new method for controlling the selectivity of optical SWCNT sensors through colloidal templating of the exposed surface area. Colloidal nanotube sensors were obtained using various concentrations of sodium cholate, and their performances were compared to DNA-SWCNT optical sensors. Sensor responses were measured against a library of bioanalytes, including neurotransmitters, amino acids, and sugars. We report an intensity response towards dopamine and serotonin for all sodium cholate-suspended SWCNT concentrations. We further identify a selective, 14.1 nm and 10.3 nm wavelength red-shifting response to serotonin for SWCNTs suspended in 1.5 and 0.5 mM sodium cholate, respectively. Through controlled, adsorption-based tuning of the nanotube surface, this study demonstrates the applicability of sub-critical colloidal suspensions to achieve selectivities exceeding those previously reported for DNA-SWCNT sensors.

Fluorescent Single-Walled Carbon Nanotubes for Protein Detection

Nanosensors have a central role in recent approaches to molecular recognition in applications like imaging, drug delivery systems, and phototherapy. Fluorescent nanoparticles are particularly attractive for such tasks owing to their emission signal that can serve as optical reporter for location or environmental properties. Single-walled carbon nanotubes (SWCNTs) fluoresce in the near-infrared part of the spectrum, where biological samples are relatively transparent, and they do not photobleach or blink. These unique optical properties and their biocompatibility make SWCNTs attractive for a variety of biomedical applications. Here, we review recent advancements in protein recognition using SWCNTs functionalized with either natural recognition moieties or synthetic heteropolymers. We emphasize the benefits of the versatile applicability of the SWCNT sensors in different systems ranging from single-molecule level to in-vivo sensing in whole animal models. Finally, we discuss challenges, opportunities, and future perspectives.

Non-covalent Methods of Engineering Optical Sensors Based on Single-Walled Carbon Nanotubes

Optical sensors based on single-walled carbon nanotubes (SWCNTs) demonstrate tradeoffs that limit their use in in vivo and in vitro environments. Sensor characteristics are primarily governed by the non-covalent wrapping used to suspend the hydrophobic SWCNTs in aqueous solutions, and we herein review the advantages and disadvantages of several of these different wrappings. Sensors based on surfactant wrappings can show enhanced quantum efficiency, high stability, scalability, and diminished selectivity. Conversely, sensors based on synthetic and bio-polymer wrappings tend to show lower quantum efficiency, stability, and scalability, while demonstrating improved selectivity. Major efforts have focused on optimizing sensors based on DNA wrappings, which have intermediate properties that can be improved through synthetic modifications. Although SWCNT sensors have, to date, been mainly engineered using empirical approaches, herein we highlight alternative techniques based on iterative screening that offer a more guided approach to tuning sensor properties. These more rational techniques can yield new combinations that incorporate the advantages of the diverse nanotube wrappings available to create high performance optical sensors.

Advanced biomedical applications of carbon nanotube

With advances in nanotechnology, the applications of nanomaterial are developing widely and greatly. The characteristic properties of carbon nanotubes (CNTs) make them the most selective candidate for various multi-functional applications. The greater surface area of the CNTs in addition to the capability to manipulate the surfaces and dimensions has provided greater potential for this nanomaterial. The CNTs possess greater potential for applications in biomedicine due to their vital electrical, chemical, thermal, and mechanical properties. The unique properties of CNT are exploited for numerous applications in the biomedical field. They are useful in both therapeutic and diagnostic applications. They form novel carrier systems which are also capable of site-specific delivery of therapeutic agents. In addition, CNTs are of potential application in biosensing. Many recently reported advanced systems of CNT could be exploited for their immense potential in biomedicine in the future.