skip to main content

Attention:

The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 11:00 PM ET on Friday, April 12 until 2:00 AM ET on Saturday, April 13 due to maintenance. We apologize for the inconvenience.


Title: Switchable inhibitory behavior of divalent magnesium ion in DNA hybridization-based gene quantification
Contrary to the understanding that divalent cations only result in under-estimation of gene quantification via DNA hybridization-based assays, we have discovered that Mg 2+ could cause either under or over-estimation at different concentrations. Its switchable inhibitory behavior is likely due to its rigid first solvation (hydrated) shell and hence it is inclined to form non-direct binding with DNA. At low concentrations, it caused under-estimation by occupying the hybridization sites. At high concentrations, it caused probe, signaling and target DNA to aggregate non-specifically via Coulomb forces. By quantifying target DNAs at a range of Mg 2+ concentrations using a gene quantification assay (NanoGene assay), a Mg 2+ inflection concentration of ∼10 −3 M was observed for both target ssDNA and dsDNA. Field emission scanning electron microscopy (FE-SEM), energy dispersive X-ray spectroscopy (EDS), and Fourier transform infrared spectroscopy (FT-IR) were employed to observe Mg 2+ -induced non-specific binding in the complexes that mimicked the presence of target DNA. Together with two other divalent cations Ca 2+ and Cu 2+ , they were further examined via zeta potential measurements as well as NanoGene assay. This study revealed the importance of Mg 2+ in achieving accurate gene quantification. Through a better mechanistic understanding of this phenomenon, it will be possible to develop strategies to mitigate the impact of Mg 2+ on DNA hybridization-based gene quantification.  more » « less
Award ID(s):
1922687
NSF-PAR ID:
10446620
Author(s) / Creator(s):
; ; ; ;
Date Published:
Journal Name:
The Analyst
Volume:
147
Issue:
21
ISSN:
0003-2654
Page Range / eLocation ID:
4845 to 4856
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract The coronavirus disease 2019 (COVID-19) is a highly contagious and fatal disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In general, the diagnostic tests for COVID-19 are based on the detection of nucleic acid, antibodies, and protein. Among different analytes, the gold standard of the COVID-19 test is the viral nucleic acid detection performed by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) method. However, the gold standard test is time-consuming and requires expensive instrumentation, as well as trained personnel. Herein, we report an ultrasensitive electrochemical biosensor based on zinc sulfide/graphene (ZnS/graphene) nanocomposite for rapid and direct nucleic acid detection of SARS-CoV-2. We demonstrated a simple one-step route for manufacturing ZnS/graphene by employing an ultrafast (90 s) microwave-based non-equilibrium heating approach. The biosensor assay involves the hybridization of target DNA or RNA samples with probes that are immersed into a redox active electrolyte, which are detectable by electrochemical measurements. In this study, we have performed the tests for synthetic DNA samples and, SARS-CoV-2 standard samples. Experimental results revealed that the proposed biosensor could detect low concentrations of all different SARS-CoV-2 samples, using such as S, ORF 1a, and ORF 1b gene sequences as targets. This microwave-synthesized ZnS/graphene-based biosensor could be reliably used as an on-site, real-time, and rapid diagnostic test for COVID-19. 
    more » « less
  2. Cryogenic infrared vibrational spectroscopy of D2-tagged cyanobenzoate (CBA) derivatives are obtained and analyzed to characterize the intrinsic spectroscopic responses of the -CO2‾ head group to its location on the ring in both the isolated anions and the cationic complexes with divalent metal ions, M2+ (M=Mg, Ca, Sr). The benzonitrile functionality establishes the different ring isomers (para, meta, ortho) according to the location of the carboxylate and provides an additional reporter on the molecular response to the proximal charge center. The aromatic carboxylates display slightly smaller shifts than those observed for a related aliphatic system upon metal ion complexation. Although the CBA anions display very similar band patterns for all three ring positions, upon complexation with metal ions, the ortho isomer yields dramatically different spectral responses in both the -CO2‾ moiety and the CN group. This behavior is traced to the emergence of a tridentate binding motif unique to the ortho isomer in which the metal ions bind to both the oxygen atoms of the carboxylate group and the N atom of the cyano group. In that configuration, the -CO2‾ moiety is oriented perpendicular to the phenyl ring, and the CN stretching fundamental is both strong and red-shifted relative to its behavior in the isolated neutral. The behaviors of the metal-bound ortho complexes occur in contrast to the usual blue shifts associated with “Lewis” type binding of metal ions end-on to -CN. The origins of these spectroscopic features are analyzed with the aid of electronic structure calculations, which also explore differences expected for complexation of monovalent cations to the ortho carboxylate. The resulting insights have implications for understanding the balance between electrostatic and steric interactions at metal binding sites in chemical and biological systems. 
    more » « less
  3. Deep sea biology is known to thrive at pressures up to ≈1 kbar, which motivates fundamental biophysical studies of biomolecules under such extreme environments. In this work, the conformational equilibrium of the lysine riboswitch has been systematically investigated by single molecule FRET (smFRET) microscopy at pressures up to 1500 bar. The lysine riboswitch preferentially unfolds with increasing pressure, which signals an increase in free volume (Δ V 0 > 0) upon folding of the biopolymer. Indeed, the effective lysine binding constant increases quasi-exponentially with pressure rise, which implies a significant weakening of the riboswitch–ligand interaction in a high-pressure environment. The effects of monovalent/divalent cations and osmolytes on folding are also explored to acquire additional insights into cellular mechanisms for adapting to high pressures. For example, we find that although Mg 2+ greatly stabilizes folding of the lysine riboswitch (ΔΔ G 0 < 0), there is negligible impact on changes in free volume (ΔΔ V 0 ≈ 0) and thus any pressure induced denaturation effects. Conversely, osmolytes (commonly at high concentrations in deep sea marine species) such as the trimethylamine N -oxide (TMAO) significantly reduce free volumes (ΔΔ V 0 < 0) and thereby diminish pressure-induced denaturation. We speculate that, besides stabilizing RNA structure, enhanced levels of TMAO in cells might increase the dynamic range for competent riboswitch folding by suppressing the pressure-induced denaturation response. This in turn could offer biological advantage for vertical migration of deep-sea species, with impacts on food searching in a resource limited environment. 
    more » « less
  4. Abstract The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing, the effects of tension weaker than 5 pN are less clear. In this study, we developed a DNA bow assay, which uses the bending rigidity of double-stranded DNA (dsDNA) to exert weak tension on a single-stranded DNA (ssDNA) target in the range of 2–6 pN. Combining this assay with single-molecule FRET, we measured the hybridization and dehybridization kinetics between a 15 nt ssDNA under tension and a 8–9  nt oligonucleotide, and found that both the hybridization and dehybridization rates monotonically increase with tension for various nucleotide sequences tested. These findings suggest that the nucleated duplex in its transition state is more extended than the pure dsDNA or ssDNA counterpart. Based on coarse-grained oxDNA simulations, we propose that this increased extension of the transition state is due to steric repulsion between the unpaired ssDNA segments in close proximity to one another. Using linear force-extension relations verified by simulations of short DNA segments, we derived analytical equations for force-to-rate conversion that are in good agreement with our measurements. 
    more » « less
  5. Three triorganotin (IV) cyclopentane carboxylates were synthesized and structurally characterized by in solid state by Fourier‐transform infrared spectroscopy and single crystal diffraction, and in solution by NMR (1H,13C, and119Sn) spectroscopy. The complexes were tested for their anticancer activity against MCF‐7 and HeLa cells along with normal BHK‐21 cells. As revealed by MTT assay, complex2was identified as the most potent derivative with an IC50value of 2.59 and 0.051 μM against HeLa and MCF‐7 cells, respectively. The results were compared with cisplatin as reference drug. Fluorescent microscopic studies using 4′,6‐diamidino‐2‐phenylindole (DAPI) and propidium iodide (PI) staining confirmed the occurrence of apoptosis in HeLa cells treated with the most active complex2. The complex2also triggered the release of lactate dehydrogenase (LDH) in treated HeLa and MCF‐7 cells whereas a luminescence assay displayed a remarkable increase in the activity of caspase‐9 and ‐3. Moreover, flow cytometric results revealed that complex2caused G0/G1 arrest in the treated HeLa cells. The complexes were further screened for DNA binding studies through UV‐vis spectroscopy and cyclic voltammetry. The high activity of complex2was attributed to its higher Lewis acidity as indicated by natural bond orbital (NBO) analysis. Theoretical modelling and molecular docking studies were also conducted to study the reactivity of complexes againstVEGFR 2 Kinase.

     
    more » « less