Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

Abstract

We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

Mimic uracil–uracil base pairing: self-assembly and single crystal structure

“…31 However, there are few experimental and structural data on native nucleotide molecules. 10 Here, by using aromatic ligands and cobalt or cadmium transition metals, a hydrophobic space is constructed during the…”

“…31 However, there are few experimental and structural data on native nucleotide molecules. 10 Here, by using aromatic ligands and cobalt or cadmium transition metals, a hydrophobic space is constructed during the coordination process, which induces the formation of U-motifs. 32–34 For the convenience of our study, a structural overview of the five U-motif types is presented in Fig.…”

“…8,9 Numerous non-classical base pairs, involving at least two hydrogen bonds between any two bases except for the Watson-Crick base pairs, have been discovered based on diverse characterizations, which are of great significance in revealing genetic diseases and DNA rearrangements. [10][11][12][13] However, among these characterizations, only single crystal X-ray diffraction (SC-XRD) can offer welldefined structural information, enabling the precise determination of the protonation position of the nucleobase, the hydrogen bond geometry, and the interaction mode between bases in the solid state. Unfortunately, the lack of a well-defined structure for non-classical base pairs hinders investigations into this issue.…”

Solidarity of the Coordination Helix and Water Helix in the Nucleotide Coordination Polymer

“…Nucleobase recognition in DNA is limited to cytosine–guanine and adenine–thymine base pairs. Still, nonclassical base pairs have been identified based on two hydrogen bonds among two bases (excluding Watson–Crick base pairs). , These nonclassical base pairs play a significant role in uncovering genetic diseases and DNA rearrangements . DNA can take on non-B-DNA forms like G-quadruplex, nucleic acid aptamers, intercalated motif, motif siRNA, synthetic DNA, and triplexes .…”

Hydrogen-Bonding Interactions of 8-Substituted Purine Derivatives

“…Gas-phase MS, thermal denaturation of double-stranded NAs, microcalorimetry, and nuclear magnetic resonance (NMR) spectroscopy − have been employed in studies of H-bonding interactions between nucleobases. NMR spectroscopy is considered the most powerful tool for providing information not only on complexation energies but also on the geometries of H-bonded complexes. ,, In addition to experimental studies, bonding interactions between nucleobases have been extensively studied using computational methods. − …”