Synthesis and characterization of water-soluble carbon nanotubes from mustard soot

Carbon nanotubes (CNT) has been synthesized by pyrolysing mustard oil using an oil lamp. It was made water-soluble (wsCNT) through oxidative treatment by dilute nitric acid and was characterized by SEM, AFM, XRD, Raman and FTIR spectroscopy. The synthesized wsCNT showed the presence of several junctions and defects in it. The presence of curved graphene structure (sp2) with frequent sp3 hybridized carbon is found to be responsible for the observed defects. These defects along with the presence of di- and tri-podal junctions showed interesting magnetic properties of carbon radicals formed by spin frustration. This trapped carbon radical showed ESR signal in aqueous solution and was very stable even under drastic treatment by strong oxidizing or reducing agents. Oxidative acid treatment of CNT introduced several carboxylic acid group functionalities in wsCNT along with the nicking of the CNT at different lengths with varied molecular weight. To evaluate molecular weights of these wsCNTs, an innovative method like gel electrophoresis using high molecular weight DNA as marker was introduced

How stable are the collagen and ferritin proteins for application in bioelectronics?

One major obstacle in development of biomolecular electronics is the loss of function of biomolecules upon their surface-integration and storage. Although a number of reports on solid-state electron transport capacity of proteins have been made, no study on whether their functional integrity is preserved upon surface-confinement and storage over a long period of time (few months) has been reported. We have investigated two specific cases-collagen and ferritin proteins, since these proteins exhibit considerable potential as bioelectronic materials as we reported earlier. Since one of the major factors for protein degradation is the proteolytic action of protease, such studies were made under the action of protease, which was either added deliberately or perceived to have entered in the reaction vial from ambient environment. Since no significant change in the structural characteristics of these proteins took place, as observed in the circular dichroism and UV-visible spectrophotometry experiments, and the electron transport capacity was largely retained even upon direct protease exposure as revealed from the current sensing atomic force spectroscopy experiments, we propose that stable films can be formed using the collagen and ferritin proteins. The observed protease-resistance and robust nature of these two proteins support their potential application in bioelectronics

Ordered Self-Assembled Locked Nucleic Acid (LNA) Structures on Gold(111) Surface with Enhanced Single Base Mismatch Recognition Capability

Locked nucleic acid (LNA) is a conformationally restricted nucleic acid analogue, which is potentially a better alternative than DNA for application in the nucleic acid based biosensor technologies, due to its efficient and sequence-specific DNA/RNA detection capability and lack of molecule–surface interaction on solid surfaces, compared to DNA. We report, for the first time, a straightforward way (based on simple immersion method) of generating an ordered self-assembled LNA monolayer, which is bioactive, onto a gold(111) surface. This layer is capable of giving rise to a stronger DNA recognition signal (4–4.5 times) than its DNA counterpart, and importantly, it can differentiate between a fully complementary DNA target and that having a single base mismatch, where the mismatch discrimination ratio is almost two times compared to the ratio relevant in case of DNA-based detection. We have presented high-resolution atomic force microscopy (AFM) topographs of the well-defined one-dimensional LNA molecular ordering (few hundred nanometers long) and of the two-dimensional ordered assembly formed over a large area (7 μm × 7 μm) due to parallel positioning of the one-dimensional ordered arrangements. The effects of different parameters such as LNA concentration and incubation time on LNA self-assembly have been investigated. Further, reflection absorption infrared (RAIR) spectroscopy has been applied to obtain information about the orientation of the surface-immobilized LNA molecules for the first time. It has been found that the LNA molecules undergo an orientational transition from the “lying down” to the “upright” configuration in a time scale of few hours

Regulating the On-Surface LNA Probe Density for the Highest Target Recognition Efficiency

The recent emergence of on-surface LNA-based assays as potentially better alternatives over DNA-based approaches, due to enhanced sensitivity and target specificity, raises the need for the precise identification of the factors that control the performance of these assays. In this work, we investigated whether the probe density of fully modified ssLNA probes on the gold(111) surface could influence the target recognition capacity of the LNA sensing layer and illustrated simple means to control it, primarily by adjusting the salt concentration, nature of the cation, and pH of the immobilization buffer. It was observed that monovalent Na⁺ could more effectively control the sensor probe density compared to bivalent Mg²⁺, leading to better target recognition. Interestingly, unlike in the case of ssDNA sensor probes, the target recognition efficiency of the LNA layer at the optimum probe density was found to be almost spacer-independent, probably due to the rigidity of the LNA backbone. The optimized LNA sensor layer could discriminate single base mismatches, detect a minimum target DNA concentration of 5 nM, and sense a significant level of hybridization within a time scale of a few minutes. To our knowledge, for the first time, we identify the factors that control the on-surface LNA probe density for maximizing the performance of the LNA sensing layer

Maximizing Mismatch Discrimination by Surface-Tethered Locked Nucleic Acid Probes via Ionic Tuning

Several investigations on DNA-based nucleic acid sensors performed in the past few years point toward the requirement of an alternative nucleic acid that can detect target DNA strands more efficiently, i.e., with higher sensitivity and selectivity, and can be more robust compared to the DNA sensor probes. Locked nucleic acid (LNA), a conformationally restricted DNA analogue, is potentially a better alternative than DNA, since it is nuclease-resistant, it can form a more stable duplex with DNA in a sequence-specific manner, and it interacts less with substrate surface due to presence of a rigid backbone. In this work, we probed solid-phase dehybridization of ssDNA targets from densely packed fully modified ssLNA probes immobilized onto a gold(111) surface by fluorescence-based measurement of the “on-surface” melting temperatures. We find that mismatch discrimination can be clearly improved by applying the surface-tethered LNA probes, in comparison to the corresponding DNA probes. We show that concentration as well as type of cation (monovalent and polyvalent) can significantly influence thermal stability of the surface-confined LNA–DNA duplexes, the nature of concentration dependence contradicting the solution phase behavior. Since the ionic setting influenced the fully matched duplexes more strongly than the singly mismatched duplexes, the mismatch discrimination ability of the surface-confined LNA probes could be controlled by ionic modulations. To our knowledge, this is the first report on ionic regulation of melting behavior of surface-confined LNA–DNA duplexes

Enhancing On-Surface Mismatch Discrimination Capability of PNA Probes by AuNP Modification of Gold(111) Surface

Unambiguous identification of single base mismatches in nucleic acid sequences is of great importance in nucleic acid detection assays. However, ambiguities are often encountered with, and therefore, a strategy for attaining substantially large enhancement of mismatch discrimination has been worked upon in this study. Short single-stranded peptide nucleic acid (PNA) and deoxyribonucleic acid (DNA) sensor probes that are immobilized onto gold nanoparticle (AuNP) modified Au(111) surface have been applied for target DNA detection. It will be shown that while both PNA and the analogous DNA probes exhibit generally better target detection abilities on the AuNP-modified Au(111) surface (elicited from fluorescence-based measurement of on-surface <i>T</i>_m values), compared to the bare Au(111) surface, PNA supersedes DNA, for all sizes of AuNPs (10, 50, and 90 nm) applied, with the difference being quite drastic in the case of the smallest 10 nm AuNP. It is found that while the AuNP curvature plays a pivotal role in target detection abilities of the PNA probes, the changes in the surface roughness caused by AuNP treatment do not exert any significant influence. This study also presents a means for preparing PNA–AuNP hybrids without altering PNA functionality and without AuNP aggregation by working with the surface-affixed AuNPs

Nanoscale On-Silico Electron Transport via Ferritins

Silicon is a solid-state semiconducting material that has long been recognized as a technologically useful one, especially in electronics industry. However, its application in the next-generation metalloprotein-based electronics approaches has been limited. In this work, the applicability of silicon as a solid support for anchoring the iron-storage protein ferritin, which has a semiconducting iron nanocore, and probing electron transport via the ferritin molecules trapped between silicon substrate and a conductive scanning probe has been investigated. Ferritin protein is an attractive bioelectronic material because its size (X-ray crystallographic diameter ∼12 nm) should allow it to fit well in the larger tunnel gaps (>5 nm), fabrication of which is relatively more established, than the smaller ones. The electron transport events occurring through the ferritin molecules that are covalently anchored onto the MPTMS-modified silicon surface could be detected at the molecular level by current-sensing atomic force spectroscopy (CSAFS). Importantly, the distinct electronic signatures of the metal types (i.e., Fe, Mn, Ni, and Au) within the ferritin nanocore could be distinguished from each other using the transport band gap analyses. The CSAFS measurements on holoferritin, apoferritin, and the metal core reconstituted ferritins reveal that some of these ferritins behave like n-type semiconductors, while the others behave as p-type semiconductors. The band gaps for the different ferritins are found to be within 0.8 to 2.6 eV, a range that is valid for the standard semiconductor technology (e.g., diodes based on p–n junction). The present work indicates effective on-silico integration of the ferritin protein, as it remains functionally viable after silicon binding and its electron transport activities can be detected. Potential use of the ferritin–silicon nanohybrids may therefore be envisaged in applications other than bioelectronics, too, as ferritin is a versatile nanocore-containing biomaterial (for storage/transport of metals and drugs) and silicon can be a versatile nanoscale solid support (for its biocompatible nature)