Occurrence and stability of lone pair-π and OH–π interactions between water and nucleobases in functional RNAs

Kalra, Kanav; Gorle, Suresh; Cavallo, Luigi; Oliva, Romina; Chawla, Mohit

doi:10.1093/nar/gkaa345

Cited by 33 publications

(29 citation statements)

References 94 publications

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“…Finally, we underline that imidazole represents the five-membered ring moiety of all purine nucleobases and related natural or synthetic purine nucleosides. Thus, the O-H•••π interaction here reported provides further support to a very recent investigation emphasizing such interactions between water and nucleobase in functional RNAs [40].…”

Section: Discussionsupporting

confidence: 88%

H-Bonds, π-Stacking and (Water)O-H/π Interactions in (µ4-EDTA)Bis(Imidazole) Dicopper(II) Dihydrate

et al. 2021

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We synthesized and studied the polymeric compound {[Cu2(µ4-EDTA)(Him)2] 2H2O}n (1). The single-crystal structure is reported along with an in depth characterization of its thermal stability (TGA), spectral properties (FT-IR, Vis-UV and RSE), and magnetic behavior. The crystal consists of infinite 2D-networks built by centrosymmetric dinuclear motifs, constructed by means of a bridging anti,syn-carboxylate group from each asymmetric unit. Each layer guides Him ligands toward their external faces. They are connected by intermolecular (Him)N-H···O(carboxylate) bonds and antiparallel π–π stacking between symmetry related pairs of Him ligands, and then pillared in a 3D-network with parallel channels, where disordered water molecules are guested. About half of the labile water is lost from these channels over a wide temperature range (r.t. to 210 °C) before the other one, most strongly retained by the cooperating action of (water)O1-H(1A)···O(carboxylate) and (water) O1-H(1B)···π(Him) interactions. The latter is lost when organic ligands start to burn. ESR spectra and magnetic measurements indicated that symmetry related Cu(II) centers connected by the bridging carboxylate groups behave magnetically not equivalently, enabling an exchange interaction larger than their individual Zeeman energies.

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Section: Discussionsupporting

confidence: 88%

H-Bonds, π-Stacking and (Water)O-H/π Interactions in (µ4-EDTA)Bis(Imidazole) Dicopper(II) Dihydrate

et al. 2021

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“…Following variable temperature FFC NMR relaxometry experiments [22], it was shown that water molecules can interact with pore boundaries by the inner-sphere mechanism, thereby suggesting that water molecules penetrate into biochar pores and adhere to the surface by formation of weak bonds such as non-conventional H-bonds (e.g., the OH-π bonding described in References [197,198]), Van der Waals interactions, and coordination linkages (Figure 14). The latter are Lewis acid-base interactions occurring when the electron-rich oxygen in water approaches the metal ions situated on the biochar surface.…”

Section: The Dynamics Of Water and Nutrients In Biochar Pore Systemmentioning

confidence: 99%

Recent Developments in Understanding Biochar’s Physical–Chemistry

et al. 2021

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Biochar is a porous material obtained by biomass thermal degradation in oxygen-starved conditions. It is nowadays applied in many fields. For instance, it is used to synthesize new materials for environmental remediation, catalysis, animal feeding, adsorbent for smells, etc. In the last decades, biochar has been applied also to soils due to its beneficial effects on soil structure, pH, soil organic carbon content, and stability, and, therefore, soil fertility. In addition, this carbonaceous material shows high chemical stability. Once applied to soil it maintains its nature for centuries. Consequently, it can be considered a sink to store atmospheric carbon dioxide in soils, thereby mitigating the effects of global climatic changes. The literature contains plenty of papers dealing with biochar’s environmental effects. However, a discrepancy exists between studies dealing with biochar applications and those dealing with the physical-chemistry behind biochar behavior. On the one hand, the impression is that most of the papers where biochar is tested in soils are based on trial-and-error procedures. Sometimes these give positive results, sometimes not. Consequently, it appears that the scientific world is divided into two factions: either supporters or detractors. On the other hand, studies dealing with biochar’s physical-chemistry do not appear helpful in settling the factions’ problem. This review paper aims at collecting all the information on physical-chemistry of biochar and to use it to explain biochar’s role in different fields of application.

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“…Besides the Watson–Crick pairs, early studies showed the C–H H-bonds could not be dismissed due to their frequent observation in RNA structure and their surprising stability[ 35 ]; and recent studies identified two types of π interactions in nature from over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules [ 36 ]. The C–H H-bonds could even be measured by atomic force microscopy although it’s relatively weak [ 37 ].…”

Section: Resultsmentioning

confidence: 99%

Cryo-EM structure of Mycobacterium tuberculosis 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides

Zhang

Sun

et al. 2022

Emerging Microbes & Infections

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Tuberculosis (TB) is the leading infectious disease caused by Mycobacterium tuberculosis ( Mtb ). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were previously reported to bind to the nascent polypeptide exit tunnel (NPET) near peptidyl transferase center (PTC), but the only available CTY structure in complex with D. radiodurans ( Dra ) ribosome could be misinterpreted due to resolution limitation. To date, the mechanism of specificity and efficacy of CTY for Mtb remains elusive since the Mtb ribosome-CTY complex structure is still unknown. Here, we employed new sample preparation methods and solved the Mtb ribosome-CTY complex structure at 3.3Å with cryo-EM technique, where the crucial gate site A2062 ( E. coli numbering) is located at the CTY binding site within NPET. Two alternative conformations of A2062, a novel syn -conformation as well as a swayed conformation bound with water molecule at interface, may play a role in coordinating the binding of specific drug molecules. The previously overlooked C–H hydrogen bond (H-bond) and π interaction may collectively contribute to the enhanced binding affinity. Together, our structure data provide a structural basis for the dynamic binding as well as the specificity of CTY and explain of how a single methyl group in CTY improves its potency, which provides new evidence to reveal previously unclear mechanism of translational modulation for future drug design and anti-TB therapy. Furthermore, our sample preparation method may facilitate drug discovery based on the complexes with low water solubility drugs by cryo-EM technique.

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Occurrence and stability of lone pair-π and OH–π interactions between water and nucleobases in functional RNAs

Cited by 33 publications

References 94 publications

H-Bonds, π-Stacking and (Water)O-H/π Interactions in (µ4-EDTA)Bis(Imidazole) Dicopper(II) Dihydrate

H-Bonds, π-Stacking and (Water)O-H/π Interactions in (µ4-EDTA)Bis(Imidazole) Dicopper(II) Dihydrate

Recent Developments in Understanding Biochar’s Physical–Chemistry

Cryo-EM structure of Mycobacterium tuberculosis 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides

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