An official website of the United States government
Abstract Suzuki−Miyaura cross‐coupling reactions are used to modify the tyrosine residues onBombyx morisilkworm silk proteins using a water‐soluble palladium catalyst. First, model reactions using tyrosine derivatives are screened to determine optimal reaction conditions. For these reactions, a variety of aryl boronic acids, solvents, buffers, and temperature ranges are explored. Qualitative information on the reaction progress is collected via high‐performance liquid chromatography (HPLC), mass spectrometry (MS), and nuclear magnetic resonance (NMR). Optimized reactions are then applied to silk proteins. It is demonstrated the ability to modify silk fibroin in solution by first iodinating the tyrosine residues on the protein, and then carrying out Suzuki‐Miyaura reactions with a variety of boronic acid derivatives. Modification of silk is confirmed with NMR, ion‐exchange chromatography (IEC), UV‐vis, and infrared spectroscopy (IR).
more »
« less
Determination of optical density (OD) of oligodeoxynucleotide from HPLC peak area
Oligodeoxynucleotides (ODNs) are typically purified and analysed with HPLC equipped with a UV-Vis detector. Quantities of ODNs are usually determined using a UV-Vis spectrometer separately after HPLC, and are reported as optical density at 260 nm (OD 260 ). Here, we describe a method for direct determination of OD 260 of ODNs using the area of the peaks in HPLC profiles. It is expected that the method will save significant time for researchers in the area of nucleic acid research, and minimize the loss of oligonucleotide samples.
more »
« less
- Award ID(s):
- 1954041
- PAR ID:
- 10346662
- Date Published:
- Journal Name:
- PeerJ Analytical Chemistry
- Volume:
- 4
- ISSN:
- 2691-6630
- Page Range / eLocation ID:
- e20
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract PremiseThe extraction of high‐quality RNA is the critical first step for the analysis of gene expression and gene space. This remains particularly challenging in plants, and especially in ferns, where the disruption of the cell wall and separation of organic compounds from nucleic acids is not trivial. MethodsWe developed a cetyltrimethylammonium bromide (CTAB)‐based RNA extraction protocol that consistently performs well across a large phylogenetic breadth of ferns—a lineage of plants high in secondary compounds—and in an array of tissue types. Two alternative options (precipitation vs. clean‐up without intermediate precipitation) are presented, both of which yield high‐quality RNA extracts with optical density (OD) ratios of OD 260/280 = 1.9–2.1 and OD 260/230 > 1.6, and RNA integrity numbers >7. ConclusionsThis study presents an efficient protocol for the extraction of high‐quality RNA from multiple tissues and across the fern phylogeny, a clade of plants that still lags behind other major lineages in the development of genomic resources. We hope that this method can be used to help facilitate the closing of this gap.more » « less
-
Evaluating surface bacterial growth at buried interfaces can be problematic due to the difficulties associated with obtaining samples. In this work, we present a new method to detect signals from microorganisms at buried interfaces that is nondestructive and can be conducted continuously. Inspired by vascular systems in nature that permit chemical communication between the surface and underlying tissues of an organism, we created a system in which an inert carrier fluid could be introduced into an empty vascular network embedded in a polymer matrix. When a microorganism layer was grown on top, small molecules produced by the growth process would diffuse down into the carrier fluid, which could then be collected and analyzed. We used this system to nondestructively detect signals from a surface layer of Escherichia coli using conductivity, ultraviolet–visible (UV–vis) absorbance spectroscopy, and high-performance liquid chromatography (HPLC) for organic acids, methods that ranged in sensitivity, time-to-result, and cost. Carrier fluid from sample vascularized polymers with surface bacterial growth recorded significantly higher values in both conductivity and absorbance at 350 nm compared to controls with no bacteria after 24 h. HPLC analysis showed three clear peaks that varied between the samples with bacteria and the controls without. Tests tracking the change in signals over 48 h showed clear trends that matched the bacterial growth curves, demonstrating the system’s ability to monitor changes over time. A 2D finite element model of the system closely matched the experimental results, confirming the predictability of the system. Finally, tests using clinically relevant Staphylococcus aureus and Pseudomonas aeruginosa yielded differences in conductivity, absorbance, and HPLC peak areas unique to each species. This work lays the foundation for the use of vascularized polymers as an adaptive system for the continuous, nondestructive detection of surface microorganisms at buried interfaces in both industry and medicine.more » « less
-
Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and have difficulty to produce sequences containing stable secondary structures. Here, we report a direct de novo chemical synthesis of 400 nt ODNs, and their isolation from the complex reaction mixture using the catching-by-polymerization (CBP) method. To determine the authenticity of the ODNs, 399 and 401 nt ODNs were synthesized and purified with CBP. The two were joined together using Gibson assembly to give the 800 nt green fluorescent protein (GFP) gene construct. The sequence of the construct was verified via Sanger sequencing. To demonstrate the potential use of the long ODN synthesis method, the GFP gene was expressed inE. coli. The long ODN synthesis and isolation method presented here provides a pathway to the production of genes and genomes containing long repeats or stable secondary structures that cannot be produced or are highly challenging to produce using existing technologies.more » « less
-
Colloidal quantum dots/graphene (QD/Gr) nanohybrids have been studied intensively for photodetection in a broadband spectrum including ultraviolet, visible, near-infrared, and shortwave infrared (UV−vis-NIR-SWIR). Since the optoelectronic process in the QD/Gr nanohybrid relies on the photogenerated charge carrier transfer from QDs to graphene, understanding the role of the QD−QD and QD−Gr interfaces is imperative to the QD/Gr nanohybrid photodetection. Herein, a systematic study is carried out to probe the effect of these interfaces on the noise, photoresponse, and specific detectivity in the UV−vis-NIR-SWIR spectrum. Interestingly, the photoresponse has been found to be negligible without a 3-mercaptopropionic acid (MPA) ligand exchange, moderate with a single ligand exchange after all QD layers are deposited on graphene, and maximum if it is performed after each QD layer deposition up to five layers of total QD thickness of 260−280 nm. Furthermore, exposure of graphene to C-band UV (UVC) for a short period of 4−5 min before QD deposition leads to improved photoresponse via removal of polar molecules at the QD/Gr interface. With the combination of the MPA ligand exchange and UVC exposure, optimal optoelectronic properties can be obtained on the PbS QD/Gr nanohybrids with high specific detectivity up to 2.6 × 1011, 1.5 × 1011, 5 × 1010, and 1.9 × 109 Jones at 400, 550, 1000, and 1700 nm, respectively, making the nanohybrids promising for broadband photodetection.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.7717/peerj-achem.20
