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Gulland, Jordan and Creeth. Top left: J.M. Gulland, from a photograph taken at the 1947 Symposia Nucleic Acids and Nucleoproteins. Courtesy of Cold Spring Harbor Laboratory Library and Archives. Top right: D.O. Jordan. Bottom: J.M. Creeth, photograph taken ca. 1947.
Source publication
We recall the experimental approaches involved in the discovery of hydrogen bonds in
deoxyribonucleic acid (DNA) made 70 years ago by a team of scientists at University
College Nottingham led by J.M. Gulland, and in relation to previous studies. This discovery proved an important step in the elucidation of the correct structure for DNA made by J.D....
Contexts in source publication
Context 1
... Mike Creeth's own words, looking back after his retirement [47]: 'In hindsight, we had been given not just a glimpse, but a good view of that particular bonding that is nothing less than the key to life on this planet.' He, and his distinguished supervisors Gulland and Jordan (Figure 7), and fellow students Threlfall and Taylor, helped pave the way for the final discovery by Watson and Crick of the structure of the macromolecule that is the key to life, but, characteristically, was too modest to say that. ...
Context 2
... Mike Creeth's own words, looking back after his retirement [47]: 'In hindsight, we had been given not just a glimpse, but a good view of that particular bonding that is nothing less than the key to life on this planet.' He, and his distinguished supervisors Gulland and Jordan (Figure 7), and fellow students Threlfall and Taylor, helped pave the way for the final discovery by Watson and Crick of the structure of the macromolecule that is the key to life, but, characteristically, was too modest to say that. ...
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In the present work, we investigate the double proton transfer (DPT) tautomerization process in Guanine-Cytosine (GC) DNA base pairs. In particular, we study the influence of the biological environment on the mechanism, the kinetics and thermodynamics of such DPT. To this end, we present a molecular dynamics (MD) study in the tight-binding density...
Citations
... Although not widely credited, Jordan played an important part in the history of molecular biology. Together with his colleague Masson Gulland and PhD student Mike Creeth, in 1947, Jordan discovered the hydrogen-bonded basepairing of the DNA structure (Creeth et al. 1947;Harding et al. 2018). This was five years before Watson and Crick's publication of their double-helical DNA structure (Watson and Crick 1953). ...
This article of the continuing “Biophysical Reviews Meet the Editors Series” introduces Ronald Clarke, biophysical chemist, member of the Biophysical Reviews editorial board and current Secretary-General of the International Union of Pure and Applied Biophysics (IUPAB).
... As shown in Figure 1a, DNA strands are composed of several deoxyribonucleotides polymerized by 3 →5 phosphodiester bonds, with a basic backbone formed by alternating deoxyribose and phosphate connections on the outer side and four kinds of bases (adenine, guanine, cytosine, and thymine) on the inner side. The bases between the two chains are connected by hydrogen bonds to form base pairs [2]. Drug molecules can affect or damage the structure of DNA through different pathways, which in turn directly or indirectly impede the normal DNA replication, transcription, and other processes, and eventually cause apoptosis to exert anti-tumor effects [3,4]. ...
Bendamustine (BENDA) is a bifunctional alkylating agent with alkylating and purinergic antitumor activity, which exerts its anticancer effects by direct binding to DNA, but the detailed mechanism of BENDA–DNA interaction is poorly understood. In this paper, the interaction properties of the anticancer drug BENDA with calf thymus DNA (ctDNA) were systematically investigated based on surface-enhanced Raman spectroscopy (SERS) technique mainly using a novel homemade AuNPs/ZnCl2/NpAA (NpAA: nano porous anodic alumina) solid-state substrate and combined with ultraviolet–visible spectroscopy and molecular docking simulation to reveal the mechanism of their interactions. We experimentally compared and studied the SERS spectra of ctDNA, BENDA, and BENDA–ctDNA complexes with different molar concentrations (1:1, 2:1, 3:1), and summarized their important characteristic peak positions, their peak position differences, and hyperchromic/hypochromic effects. The results showed that the binding modes include covalent binding and hydrogen bonding, and the binding site of BENDA to DNA molecules is mainly the N7 atom of G base. The results of this study help to understand and elucidate the mechanism of BENDA at the single-molecule level, and provide guidance for the further development of effective new drugs with low toxicity and side effects.
... The notion that canonical H-bonds (i.e., between electronegative groups) may play a role in DNA structure was first put forward based on biophysical studies of DNA in solution in the 1940s [151,152]. However, it was Watson and Crick who first proposed that these bonds are responsible for the complementary association of two antiparallel strands of DNA through the specific pairing of GC and AT [81,153]. ...
Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.
... 1,2 Hydrogen bonding (H-bonding) is the most important intermolecular interaction conferring structural stability to proteins, DNA, and other macromolecules. 3,4 Elfi Kraka et al. in a recent work studied H-bonding in a diverse set of natural and unnatural base pairs adenine-thymine, adenine-uracil, and guanine-cytosine using local vibrational mode study, QTAIM study, and NBO analysis. 5 Uracil (U), an important biological organic heterocyclic is a pyrimidine derivative and nucleobase in ribonucleic acid. ...
The density functional theory calculations have been applied to investigate hydrogen-bonded complexes of nicotinamide with parent uracil and its anticancer derivatives namely 5 fluorouracil and 2 thiouracil. The optimized complexes are analyzed in terms of structural, electronic, and energetic changes, binding free energy and enthalpy changes, dipole moments, atomic charge variation, electron delocalizations, topological parameters, chemical reactivity descriptors, etc. The study suggests that the most stable complexes are formed by nicotinamide with fluorouracil and the least stable with thiouracil. The uracil and its derivatives act as far better hydrogen bond donors than nicotinamide in the optimized complexes. Significant charge transfer between nicotinamide and parent uracil and its derivatives is suggested by Frontier Molecular Orbital (FMO) analysis and E(2) from Natural Bond Orbital analysis. The present computational study shows that uracil drugs form stable intercalation sites with nicotinamide. The results may prove useful in the molecular designing of new anticancer agents.
... Other essential roles played by Hydrogen bonding can be seen in binding between substrate and enzyme [5] shown by Fersht. Hydrogen bonds play a vital role in the structure of the DNA helix [5,6]. Lehn showed that hydrogen bonds help in selforganising in supramolecular chemistry [7] and Xanthes [8], Albrecht and coworkers [9] and Zabardasti and coworkers [10] showed that hydrogen bonding is involved in molecular cluster formations. ...
It has been more than a century since the discovery of hydrogen bonds, but the knowledge about its impact on day to day life of people is getting enhanced even now. It has a pivotal role in the stabilization of various biomolecules and subsequent bioactivity. Sulfur cantered hydrogen bond (SCHB), which is a weak interaction, has attracted the attention of many scientists in the last few decades. In this work, we report the nature of the SCHB between aliphatic/aromatic thiols and water. B3LYP-D3(BJ) with cc-pVTZ level was used for modeling the hydrogen bonded thiol-water complexes. Domain-based local pair natural orbitals coupled-cluster theory with single, double, and perturbative triple excitation DLPNO-CCSD(T) method was used for local energy decomposition analysis. QTAIM analysis helped to examine hydrogen bonds, weak non-covalent interactions, and the various electron density delocalization. Natural Bond Orbital (NBO) analysis explains the reason for the sulfur atom being the H-bond donor. Second-order perturbation energy from NBO findings supports the data obtained by LED and AIM calculations. Aromatic thiols form stronger hydrogen bonds than aliphatic thiols. The effect of substituents was also explored by studying aromatic systems with electron-withdrawing groups and donating groups. EDG substituted have more vital interaction, and EWG substituted thiols form stronger S-H…O hydrogen bonds.
... For symmetric hydrogen bonds, two atoms of the same chemical element (e.g, halogen atoms) are bonded to the hydrogen atom with the same interatomic distance [3,4]. The classical hydrogen bonds are very important for biological systems including the protein synthesis and structure, the DNA structure, the enzyme-substrate interaction, and so on [5][6][7]. ...
p>In previous work, we developed the local potential energy model, LPE, based on the electrostatic force and QTAIM topological data to quantify classical hydrogen bond energies. In this work, we extended the investigation to other inter/intramolecular interactions (non-conventional hydrogen bonds and others). The LPE presented high precision and linearity with supramolecular binding energy, when excluding interactions of an ion with π-bonded groups or polar molecule. The energy decomposition analysis from SAPT-DFT and LMOEDA showed that dispersion and electrostatic components are important to LPE, while polarization component impairs it. The LPE cannot be used for complexes with predominant polarization component. </p
... The HB is critical in the following cases: the folding and the final structure of the globular proteins [5]; the binding between substrate and enzyme [6]; the structure of the two strands of DNA helix; and the protein synthesis [6,7]. The HBs in -helical and -sheet model peptides were evaluated by the quantum theory of atoms in molecules, QTAIM [8], showing a linear relationship between topological data and energy of stabilization [9,10]. ...
We developed the local potential energy, LPE, model based on the electrostatic force (the unique fundamental force for chemical bonds) whose equation uses QTAIM topological data. The effectiveness of the LPE was evaluated with other well-known methods (supramolecular binding enthapy, SAPT-DFT, LMOEDA and IQA) by analyzing the hydrogen bond energy for a set of organic and inorganic molecules. The LPE has the second highest linearity with the supramolecular binding enthalpy (R²=0.9808) and the highest precision (RMSD=1.60 kcal mol⁻¹). In addition, LPE has the advantage to give individual binding energy values when the complex has more than one hydrogen bond.
... For example, compounds 54 (Sulfoxaflor) (shown in Fig. 3) and 32 (Imidacloprid) contain N-N fragment at the topological distance 7 and their corresponding pLC 50 values are 0.053 and −1.029 respectively. Both intra and intermolecular hydrogen bonds exist in DNA (Harding et al., 2018). Presence of electronegative heteroatom like nitrogen may form hydrogen bond and electron donor acceptor (EDA) complex with the DNA of earthworm. ...
Earthworm provides sustainability towards the agroecosystem which can be degraded day by day by the extensive use of pesticides (e.g., fungicides, insecticides and herbicides). The present study attempts to develop a predictive quantitative structure-activity relationship (QSAR) model for toxicity of pesticides to earthworm in order to give a suitable guidance for designing new analogues with lower toxicity by exploring the important chemical features which are required to develop safer alternatives. The QSAR model was developed by using the negative logarithm of lethal concentration (pLC50) values of pesticides towards earthworm. We have used various 2D descriptors along with extended topochemical atom (ETA) indices as independent variables for the development of the model. The developed partial least squares (PLS) model was subjected to statistical validation tests proving that the model is statistically reliable and robust (R2 = 0.765, Q2 = 0.614, Q2F1 = 0.734, Q2F2 = 0.713). The contributing descriptors in the model suggested that the pesticides may affect the earthworm nucleic acid through various physicochemical interactions including hydrophobicity, hydrogen bonding, electron donor acceptor complex formation, π-π stacking interaction and charge transfer complex formation.
Hydrogen-bonded complexes have increased donor–acceptor and acid–base properties and increased reactivity compared to monomers.
