Primary, secondary and higher-order structures of downstream elements of mammalian pre-mRNA polyadenylation signals [poly(A) signals] are re viewed. We have carried out a detailed analysis on our database of 244 human pre-mRNA poly(A) signals in order to characterize elements in their downstream regions. We suggest that the downstream region of the mammalian pre-mRNA poly(A) signal consists of various simple elements located at different distances from each other. Thus, the downstream region is not described by any precise consensus. Searching our database, we found that approximately 80% of pre-mRNAs with the AAUAAA or AUUAAA core upstream elements contain simple downstream elements, consisting of U-rich and/or 2GU/U tracts, the former occurring approximately 2-fold more often than the latter. Approximately one-third of the pre-mRNAs analyzed here contain sequences that may form G-quadruplexes. A substantial number of these sequences are located immediately downstream of the poly(A) signal. A possible role of G-rich sequences in the polyadenylation process is discussed. A model of the secondary structure of the SV40 late pre-mRNA poly(A) signal downstream region is presented.

This study aims to cast light on the physico-chemical nature and energetic of the non-conventional CH···O/N H-bonds in the biologically important natural nucleobase pairs using a comprehensive quantum-chemical approach. As a whole, the 36 biologically important pairs, involving canonical and rare tautomers of nucleobases, were studied by means of all available up-to-date state-of-the-art quantum-chemical techniques along with quantum theory "Atoms in molecules" (QTAIM), Natural Bond Orbital (NBO) analysis, Grunenberg's compliance constants theory, geometrical and vibrational analyses to identify the CH···O/N interactions, reveal their physico-chemical nature and estimate their strengths as well as contribution to the overall base-pairs stability. It was shown that all the 38 CH···O/N contacts (25 CH···O and 13 CH···N H-bonds) completely satisfy all classical geometrical, electron-topological, in particular Bader's and "two-molecule" Koch and Popelier's, and vibrational criteria of H-bonding. The positive values of Grunenberg's compliance constants prove that the CH···O/N contacts in nucleobase pairs are stabilizing interactions unlike electrostatic repulsion and anti-H-bonds. NBO analysis indicates the electron density transfer from the lone electron pair of the acceptor atom (O/N) to the antibonding orbital corresponding to the donor group σ(∗)(CH). Moreover, significant increase in the frequency of the out-of-plane deformation modes γ (CH) under the formation of the CH···O (by 17.2÷81.3/10.8÷84.7 cm(-1)) and CH···N (by 32.7÷85.9/9.0÷77.9 cm(-1)) H-bonds at the density functional theory (DFT)/second-order Møller-Plesset (MP2) levels of theory, respectively, and concomitant changes of their intensities can be considered as reliable indicators of H-bonding. The strengths of the CH···O/N interactions, evaluated by means of Espinosa-Molins-Lecomte formula, lie within the range 0.45÷3.89/0.62÷4.10 kcal/mol for the CH···O H-bonds and 1.45÷3.17/1.70÷3.43 kcal/mol for the CH···N H-bonds at the DFT/MP2 levels of theory, respectively. We revealed high linear mutual correlations between the H-bond energy and different physico-chemical parameters of the CH···O/N H-bonds. Based on these observations, the authors asserted that the most reliable descriptors of the H-bonding are the electron density ρ at the СН···О/N H-bond critical points and the NBO calculated stabilization energy E((2)). The linear dependence of the H-bond energy ECH···O/N (in kcal/mol) on the electron density ρ (in atomic units) was established (DFT/MP2): ECH···O = 248.501[Formula: see text]ρ-0.367/260.518[Formula: see text]ρ-0.373 and ECH···N = 218.125[Formula: see text]ρ-0.339/243.599[Formula: see text]ρ-0.441. Red-shifted and blue-shifted CH···O/N H-bonds behave in a similar way and can be described with the same fit parameters. It was found that the A-U HH2 and U-U3 nucleobase pairs are stabilized solely by the CH···O/N H-bonds. At the same time, in the A-U HH1, A-U HH2, A-Asyn 1, A-Asyn 2, A-Asyn 3, A-A4, A-G1, A-G2, G-U1, G-U2, G-U3, G-C HH1, U-U1, U-...