scholarly journals Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

2020 ◽  
Vol 48 (15) ◽  
pp. 8796-8807
Author(s):  
Romeo C A Dubini ◽  
Alexander Schön ◽  
Markus Müller ◽  
Thomas Carell ◽  
Petra Rovó
Keyword(s):  
Chemical Exchange ◽  
Epigenetic Modification ◽  
Melting Process ◽  
Chemical Exchange Saturation Transfer ◽  
Base Pairs ◽  
Fold Reduction ◽  
Modified Dna ◽  
Dna Strands ◽  
Association Rate Constants ◽  
The Impact

Abstract 5-Formylcytosine (5fC) is a chemically edited, naturally occurring nucleobase which appears in the context of modified DNA strands. The understanding of the impact of 5fC on dsDNA physical properties is to date limited. In this work, we applied temperature-dependent 1H Chemical Exchange Saturation Transfer (CEST) NMR experiments to non-invasively and site-specifically measure the thermodynamic and kinetic influence of formylated cytosine nucleobase on the melting process involving dsDNA. Incorporation of 5fC within symmetrically positioned CpG sites destabilizes the whole dsDNA structure—as witnessed from the ∼2°C decrease in the melting temperature and 5–10 kJ mol−1 decrease in ΔG°—and affects the kinetic rates of association and dissociation. We observed an up to ∼5-fold enhancement of the dsDNA dissociation and an up to ∼3-fold reduction in ssDNA association rate constants, over multiple temperatures and for several proton reporters. Eyring and van’t Hoff analysis proved that the destabilization is not localized, instead all base-pairs are affected and the transition states resembles the single-stranded conformation. These results advance our knowledge about the role of 5fC as a semi-permanent epigenetic modification and assist in the understanding of its interactions with reader proteins.

scholarly journals 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives

2021 ◽  
Author(s):  
Romeo Cosimo Arrigo Dubini ◽  
Eva Korytiaková ◽  
Thea Schinkel ◽  
Pia Heinrichs ◽  
Thomas Carell ◽  
...  
Keyword(s):  
Base Pair ◽  
Chemical Exchange ◽  
Excision Repair ◽  
Epigenetic Modification ◽  
Conformational Exchange ◽  
Epigenetic Mark ◽  
Dna Strands ◽  
Domains Of Life ◽  
Base Excision ◽  
The Impact

5-carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ≈10-20 kJ mol-1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the µs time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC's subtle sensitivity to acidic pH contribute to the long standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.

Amide proton transfer imaging for differentiation of tuberculomas from high-grade gliomas: Preliminary experience

2021 ◽  
pp. 197140092110027
Author(s):  
Karthik Kulanthaivelu ◽  
Shumyla Jabeen ◽  
Jitender Saini ◽  
Sanita Raju ◽  
Atchayaram Nalini ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Chemical Exchange ◽  
Spin Echo ◽  
Chemical Exchange Saturation Transfer ◽  
Amide Proton ◽  
High Grade ◽  
Saturation Pulse ◽  
Amide Proton Transfer ◽  
High Grade Gliomas ◽  
Amide Protons

Purpose Tuberculomas can occasionally masquerade as high-grade gliomas (HGG). Evidence from magnetisation transfer (MT) imaging suggests that there is lower protein content in the tuberculoma microenvironment. Building on the principles of chemical exchange saturation transfer and MT, amide proton transfer (APT) imaging generates tissue contrast as a function of the mobile amide protons in tissue’s native peptides and intracellular proteins. This study aimed to further the understanding of tuberculomas using APT and to compare it with HGG. Method Twenty-two patients ( n = 8 tuberculoma; n = 14 HGG) were included in the study. APT was a 3D turbo spin-echo Dixon sequence with inbuilt B0 correction. A two-second, 2 μT saturation pulse alternating over transmit channels was applied at ±3.5 ppm around water resonance. The APT-weighted image (APTw) was computed as the MT ratio asymmetry (MTRasym) at 3.5 ppm. Mean MTRasym values in regions of interest (areas = 9 mm2; positioned in component with homogeneous enhancement/least apparent diffusion coefficient) were used for the analysis. Results MTRasym values of tuberculomas ( n = 14; 8 cases) ranged from 1.34% to 3.11% ( M = 2.32 ± 0.50). HGG ( n = 17;14 cases) showed MTRasym ranging from 2.40% to 5.70% ( M = 4.32 ± 0.84). The inter-group difference in MTRasym was statistically significant ( p < 0.001). APTw images in tuberculomas were notable for high MTRasym values in the perilesional oedematous-appearing parenchyma (compared to contralateral white matter; p < 0.001). Conclusion Tuberculomas demonstrate lower MTRasym ratios compared to HGG, reflective of a relative paucity of mobile amide protons in the ambient microenvironment. Elevated MTRasym values in perilesional parenchyma in tuberculomas are a unique observation that may be a clue to the inflammatory milieu.

scholarly journals Non-Specific Low Back Pain and Lumbar Radiculopathy: Comparison of Morphologic and Compositional MRI as Assessed by gagCEST Imaging at 3T

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 402
Author(s):  
Miriam Frenken ◽  
Sven Nebelung ◽  
Christoph Schleich ◽  
Anja Müller-Lutz ◽  
Karl Ludger Radke ◽  
...  
Keyword(s):  
Low Back Pain ◽  
Back Pain ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Chemical Exchange ◽  
Clinical Pathology ◽  
Chemical Exchange Saturation Transfer ◽  
Low Back ◽  
Intervertebral Disks ◽  
Asymptomatic Volunteers

Using glycosaminoglycan Chemical Exchange Saturation Transfer (gagCEST) magnetic resonance imaging (MRI), this study comparatively evaluated the GAG contents of lumbar intervertebral disks (IVDs) of patients with non-specific low back pain (nsLBP), radiculopathy, and asymptomatic volunteers to elucidate the association of clinical manifestation and compositional correlate. A total of 18 patients (mean age 57.5 ± 22.5 years) with radiculopathy, 16 age-matched patients with chronic nsLBP and 20 age-matched volunteers underwent standard morphologic and compositional gagCEST MRI on a 3T scanner. In all cohorts, GAG contents of lumbar IVDs were determined using gagCEST MRI. An assessment of morphologic IVD degeneration based on the Pfirrmann classification and T2-weighted sequences served as a reference. A linear mixed model adjusted for multiple confounders was used for statistical evaluation. IVDs of patients with nsLBP showed lower gagCEST values than those of volunteers (nsLBP: 1.3% [99% confidence intervals (CI): 1.0; 1.6] vs. volunteers: 1.9% [99% CI: 1.6; 2.2]). Yet, IVDs of patients with radiculopathy (1.8% [99% CI: 1.4; 2.1]) were not different from patients with nsLBP or volunteers. In patients with radiculopathy, IVDs directly adjacent to IVD extrusions demonstrated lower gagCEST values than distant IVDs (adjacent: 0.9% [99% CI: 0.3; 1.5], distant: 2.1% [99% CI: 1.7; 2.5]). Advanced GAG depletion in nsLBP and directly adjacent to IVD extrusions in radiculopathy indicates close interrelatedness of clinical pathology and compositional degeneration.

scholarly journals A generalized ratiometric chemical exchange saturation transfer (CEST) MRI approach for mapping renal pH using iopamidol

2017 ◽  
Vol 79 (3) ◽  
pp. 1553-1558 ◽  
Author(s):  
Yin Wu ◽  
Iris Y. Zhou ◽  
Takahiro Igarashi ◽  
Dario L. Longo ◽  
Silvio Aime ◽  
...  
Keyword(s):  
Chemical Exchange ◽  
Chemical Exchange Saturation Transfer ◽  
Saturation Transfer ◽  
Cest Mri
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