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Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells

G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the …

Big Changes for Small Noncovalent Dimers: Revisiting the Potential Energy Surfaces of (P2)2 and (PCCP)2 with CCSD(T) Optimizations and Vibrational Frequencies

This article details the re-examination of low-lying stationary points on the potential energy surfaces (PESs) of two challenging noncovalent homogeneous dimers, (P2)2 and (PCCP)2. The work was motivated by the rather large differences between MP2 …

Peptide Bond Formation via Glycine Condensation in the Gas Phase

Four unique gas phase mechanisms for peptide bond formation between two glycine molecules have been mapped out with quantum mechanical electronic structure methods. Both concerted and stepwise mechanisms, each leading to a cis and trans glycylglycine …

Homogeneous and Heterogeneous Noncovalent Dimers of Formaldehyde and Thioformaldehyde: Structures, Energetics, and Vibrational Frequencies

This work provides the first characterization of five stationary points of the homogeneous thioformaldehyde dimer, (CH2S)2, and seven stationary points of the heterogeneous formaldehyde/thioformaldehyde dimer, CH2O/CH2S, with correlated *ab initio* …

Epigenetic Modification, Dehydration, and Molecular Crowding Effects on the Thermodynamics of i-Motif Structure Formation from C-Rich DNA

DNA sequences with the potential to form secondary structures such as i-motifs (iMs) and G-quadruplexes (G4s) are abundant in the promoters of several oncogenes and, in some instances, are known to regulate gene expression. Recently, iM-forming DNA …

Characterization of the potential energy surfaces of two small but challenging noncovalent dimers: (P2)2 and (PCCP)2

This work characterizes eight stationary points of the P2 dimer and six stationary points of the PCCP dimer, including a newly identified minimum on both potential energy surfaces. Full geometry optimizations and corresponding harmonic vibrational …

Interstaple Dithiol Cross-Linking in Au25(SR)18 Nanomolecules: A Combined Mass Spectrometric and Computational Study

A systematic study of cross-linking chemistry of the Au25(SR)18 nanomolecule by dithiols of varying chain length, HS–(CH2)n–SH where n = 2, 3, 4, 5, and 6, is presented here. Monothiolated Au25 has six [RSAuSRAuSR] staple motifs on its surface, and …