Biology subjects

Sajjadi, S. H.

Publications and source records attributed to Sajjadi, S. H..

3 recordsLinked to original sources

bioRxiv2023

Prediction of mycotoxin response of DNA-wrapped nanotube sensor with machine learning

DNA-wrapped single-walled carbon nanotubes (DNA-SWCNTs) have demonstrated great versatility as optical sensors. SWCNTs emit a near-infrared fluorescence that is responsive to the slightest changes in their environment, enabling the creation of sensors that can respond to single-molecule fluctuations within the vicinity of their surfaces. The fluorescence response and surface interactions of these sensors are determined by the DNA wrapping sequence. However, the lack of information on the relationship between the DNA sequence and its effect on the SWCNT fluorescence remains a bottleneck for designing sensors specific to analytes of interest. The use of directed evolution was recently demonstrated in order to evolve SWCNT sensors towards mycotoxins through iterative cycles of DNA mutation, screening and selection. In the current work, we use the data acquired during the directed evolution of DNA-SWCNT sensors to train machine learning (ML) algorithms. Artificial neural network (ANN) and support vector machine (SVM) methods were used to predict the response of DNA-SWCNT sensors to the mycotoxin. The reliability of the models was assessed through cross-validation. The cross-validated ANN and SVM models were able to accurately classify the various DNA-SWCNTs as yielding either a high or low fluorescence response with an accuracy of 73 and 81%, respectively. The models were further tested on alternative similar and dissimilar DNA sequences outside of the initial training dataset. The ANN model showed a better ability to predict dissimilar DNA sequences resulting in a high sensor response in comparison with the SVM model. In addition, the possibility to combine the two SVM and ANN models with directed evolution methods was investigated. The experimental results showed that the SVM model was able to predict the response of DNA-SWCNT sensors with 95% accuracy. Finally, the Hierarchy and k-means++ clustering methods were used to examine the similarity and dissimilarity of each DNA sequence at every stage of our investigation. In this work, we show that the application of ML algorithms to directed evolution libraries of DNA allows one to accurately map the performances of DNA-SWCNT sensors within a particular DNA sequence space. Moreover, the computational success of this mapping provides a framework for replacing current empirical approaches with the rational design of DNA sequences for SWCNT sensing.

bioengineering↗

bioRxiv2023

Photoluminescence brightening of single-walled carbon nanotubes through conjugation with graphene quantum dots

Spanning the tissue transparency window, the near-infrared (NIR) photoluminescence (PL) of single-walled carbon nanotubes (SWCNTs) can optically penetrate biological tissue for deep-tissue imaging and optical sensing. SWCNTs are often functionalized with single-stranded DNA (ssDNA) to yield biocompatible, responsive, and selective sensors. However, the low brightness of these ssDNA-wrapped SWCNTs sensors restricts the depth at which such sensors can be implanted in the tissue. This work demonstrates the PL enhancement of ssDNA-wrapped SWCNTs by incorporating biocompatible graphene quantum dots (GQDs). Two kinds of GQDs, pristine (PGQDs) and nitrogen-doped (NGQDs), were fabricated and characterized. Thermodynamically, both GQDs were shown to significantly increase the fluorescence efficiency of ssDNA-SWCNTs with the same degree of PL enhancement after 3 h. Furthermore, a correlation between the diameter of the SWCNTs and the PL enhancement factor was found; the larger the SWCNT diameter, the higher the PL increase upon adding GQDs. For instance, a 30-fold enhancement was achieved for (8,6) chirality while it was only 2-fold for the (6,5) chirality. Our experiments showed that adding GQDs increases the surface coverage of SWCNTs suspended by ssDNA, limiting water molecules access to the nanotube surface, thus increasing the fluorescence efficiency. Kinetically, NGQDs brightened SWCNTs much faster than PGQDs. The PL intensity reached a plateau in 2 min following the addition of NGQDs, while it was still increasing even after 1 h upon the addition of PGQDs. We show that NGQDs can act as reducing agents to decrease the amount of dissolved oxygen, which quenches the SWCNTs PL. This advancement provides a promising tool for engineering the brightness of NIR sensors for biomedical applications such as single-molecule imaging of individual SWCNTs using NIR confocal microscopy and deep tissue sensing.

biophysics↗

bioRxiv2021

A simple micropreparative gel electrophoresis technique for purification of proteins, nucleic acids, and bioconjugates

The biochemical and biomedical fields hinge on the ability to effectively separate and purify biological macromolecules. Though this need is largely addressed with a variety of chromatographic and electrophoretic purification techniques, such techniques are usually laborious, time-consuming, and often require complex and costly instalments that are inaccessible to most laboratories. In this work, we introduce a simple micro-preparative (MP) method based on polyacrylamide gel electrophoresis (PAGE) to purify biological samples containing proteins, nucleic acids, and complex bioconjugates. Using a conventional vertical slab system, we demonstrate the extraction of purified DNA, proteins, and DNA-protein bioconjugates from their respective mixtures using MP-PAGE. We apply this system to recover DNA from a ladder mixture with yields of up to 90%, compared to the 58% yield obtained using specialized commercial devices. We also demonstrate the purification of folded enhanced yellow fluorescence protein (EYFP) from crude cell extract with 90% purity, comparable to purities achieved using a two-step size exclusion and immobilized metal-ion affinity chromatography purification procedure. Finally, we demonstrate the successful isolation of an EYFP-DNA bioconjugate sample that otherwise could not be processed using the two-step chromatography procedure. MP-PAGE thus offers a rapid and versatile means of purifying a variety of biomolecules without the need for specialized equipment.

biochemistry↗