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The inclusive J/ψ production has been studied in Pn-Pb and pp collisions at the centre-of-mass energy per nucleon pair sNN−−−√=5.02 TeV, using the ALICE detector at the CERN LHC. The J/ψ meson is reconstructed, in the centre-of-mass rapidity interval 2.5<y<4 and in the transverse-momentum range pT<12 GeV/c, via its decay to a muon pair. In this Letter, we present results on the inclusive J/ψ cross section in pp collisions at s√=5.02 TeV and on the nuclear modification factor RAA. The latter is presented as a function of the centrality of the collision and, for central collisions, as a function of the transverse momentum pT of the J/ψ. The measured RAA values indicate a suppression of the J/ψ in nuclear collisions and are then compared to our previous results obtained in Pb-Pb collisions at sNN−−−√=2.76 TeV. The ratio of the RAA values at the two energies is also computed and compared to calculations of statistical and dynamical models. The numerical value of the ratio for central events (0-10\% centrality) is 1.17±0.04(stat)±0.20(syst). In central events, as a function of pT, a slight increase of RAA with collision energy is visible in the region 2<pT<6 GeV/c. Theoretical calculations provide a good description of the measurements, within uncertainties.
A(syn)-U/T and G(syn)-C+ Hoogsteen (HG) base pairs (bps) are energetically more disfavored relative to Watson–Crick (WC) bps in A-RNA as compared to B-DNA by >1 kcal/mol for reasons that are not fully understood. Here, we used NMR spectroscopy, optical melting experiments, molecular dynamics simulations and modified nucleotides to identify factors that contribute to this destabilization of HG bps in A-RNA. Removing the 2′-hydroxyl at single purine nucleotides in A-RNA duplexes did not stabilize HG bps relative to WC. In contrast, loosening the A-form geometry using a bulge in A-RNA reduced the energy cost of forming HG bps at the flanking sites to B-DNA levels. A structural and thermodynamic analysis of purine-purine HG mismatches reveals that compared to B-DNA, the A-form geometry disfavors syn purines by 1.5–4 kcal/mol due to sugar-backbone rearrangements needed to sterically accommodate the syn base. Based on MD simulations, an additional penalty of 3–4 kcal/mol applies for purine-pyrimidine HG bps due to the higher energetic cost associated with moving the bases to form hydrogen bonds in A-RNA versus B-DNA. These results provide insights into a fundamental difference between A-RNA and B-DNA duplexes with important implications for how they respond to damage and post-transcriptional modifications.