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Transmissible spongiform encephalopathies (or prion diseases) such as Creutzfeldt-Jacob disease, mad cow disease, and scrapie are characterized by accumulation in the brain of misfolded prion protein aggregates (PrPSc) that have... 

Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011 Å and 1.060 ± 0.011 Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010 Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041 Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083 Å and 1.087 Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041 Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments. 

The majority of base pairs in double-stranded DNA exist in the canonical Watson-Crick geometry. However, they can also adopt alternate Hoogsteen conformations in various complexes of DNA with proteins and small molecules, which are key for biological function and mechanism. While detection of Hoogsteen base pairs in large DNA complexes and assemblies poses considerable challenges for traditional structural biology techniques, we show here that multidimensional dynamic nuclear polarization–enhanced solid-state NMR can serve as a unique spectroscopic tool for observing and distinguishing Watson-Crick and Hoogsteen base pairs in a broad range of DNA systems based on characteristic NMR chemical shifts and internuclear dipolar couplings. We illustrate this approach using a model 12-mer DNA duplex, free and in complex with the antibiotic echinomycin, which features two central adenine-thymine base pairs with Watson-Crick and Hoogsteen geometry, respectively, and subsequently extend it to the ∼200 kDa Widom 601 DNA nucleosome core particle. 

Lithium nickel manganese cobalt oxide (Li x Ni y Mn z Co 1−y−z O 2 , 0 < x , y , z < 1, also known as NMC) is a class of cathode materials used in lithium ion batteries. Despite the increasing use of NMC in nanoparticle form for next-generation energy storage applications, the potential environmental impact of released nanoscale NMC is not well characterized. Previously, we showed that the released nickel and cobalt ions from nanoscale Li 1/3 Ni 1/3 Mn 1/3 Co 1/3 O 2 were largely responsible for impacting the growth and survival of the Gram-negative bacterium Shewanella oneidensis MR-1 (M. N. Hang et al. , Chem. Mater. , 2016, 28 , 1092). Here, we show the first steps toward material redesign of NMC to mitigate its biological impact and to determine how the chemical composition of NMC can significantly alter the biological impact on S. oneidensis . We first synthesized NMC with various stoichiometries, with an aim to reduce the Ni and Co content: Li 0.68 Ni 0.31 Mn 0.39 Co 0.30 O 2 , Li 0.61 Ni 0.23 Mn 0.55 Co 0.22 O 2 , and Li 0.52 Ni 0.14 Mn 0.72 Co 0.14 O 2 . Then, S. oneidensis were exposed to 5 mg L −1 of these NMC formulations, and the impact on bacterial oxygen consumption was analyzed. Measurements of the NMC composition, by X-ray photoelectron spectroscopy, and composition of the nanoparticle suspension aqueous phase, by inductively coupled plasma-optical emission spectroscopy, showed the release of Li, Ni, Mn, and Co ions. Bacterial inhibition due to redesigned NMC exposure can be ascribed largely to the impact of ionic metal species released from the NMC, most notably Ni and Co. Tuning the NMC stoichiometry to have increased Mn at the expense of Ni and Co showed lowered, but not completely mitigated, biological impact. This study reveals that the chemical composition of NMC nanomaterials is an important parameter to consider in sustainable material design and usage.