The importance of avoiding potentially degradative and disruptive conditions in the extraction and purification procedure was stressed again: studies on poor-quality material which had been damaged or degraded were of limited use in connection with the nucleic acid structure. Using the samples with the requisite high quality prepared by Gulland et al.
They observed unusual behaviour with p K a values for the groups at more extreme pH values than expected: the groups failed to titrate as they would have done in free solution — indicating the possibility that, in the DNA molecule, the titratable groups may have been blocked from doing so by the formation of hydrogen bonds. The final step was made by Creeth et al. Earlier work had shown a reduction in viscosity resistance to flow on the addition of acid or alkali [ 27 ], but that reduction had been interpreted in terms of depolymerisation and had been on DNA of questionable quality see footnote to ref.
The new study [ 3 ] was performed on the same mildly isolated high-quality and molecularly intact DNA used for the titration studies. A Frampton [ 28 , 29 ] capillary viscometer was employed, which provides the advantage over conventional Ostwald capillary viscometers in being able to measure viscosity at different hydrostatic pressures.
These are apparent values corresponding to particular applied pressures or equivalent shear rates. High apparent relative viscosities were observed at a series of hydrostatic pressures, which increased as the pressure was dropped, confirming non-Newtonian behaviour. The dramatic way the high relative viscosity resistance to flow of DNA solutions dropped is shown in Figure 2 for two hydrostatic pressures at the same extremes of pH, namely below 5. These observations were reinforced by streaming birefringence measurements, which involved mechanical stirring of a solution placed in a small cell on the optical stage of a polarising microscope.
The high birefringence caused by the alignment of long polymeric molecules at neutral pH was completely lost at the same extremes of pH observed using viscometry, again through disruption of the hydrogen bonds. Starting from neutral pH 6—7 , either acid was added down to a pH of below 3. Also shown are the very different profiles for preparations of material after III alkaline pretreatment and IV acid pretreatment , and also for a sample provided by Professor Caspersson.
Redrawn from Creeth et al. Gulland's team concluded that hydrogen bonds exist between neighbouring nucleotides, and that these are disrupted by high-acid or high-alkali conditions to give units of much smaller size [ 3 ]:.
The critical pH values are coincident with those in which a liberation of amino and hydroxyl groups has been observed and it is considered that the two phenomena are related and are due to the fission of the hydrogen bonds postulated as linking the purine-pyrimidine hydroxyl groups and some of the amino-groups.
However, as to which base linked with which was not known. Furthermore — as pointed out by Booth and Hey [ 6 ] — there was also no decision at this stage that hydrogen-bonded bases on neighbouring chains led to a double-stranded structure. Initially, in the concluding remarks of the Creeth et al. Indeed, it was concluded that the data could be explained by either one or both of the following two scenarios:. However, Creeth in his PhD thesis which followed soon after [ 4 ] produced his own two-chain model for DNA, which turned out to be not too far away from the true structure.
Although the work was undertaken at University College Nottingham, because this was before the College received its Royal Charter, PhD's were officially external degrees of the University of London. The Nottingham team led by Gulland were by no means the first to isolate and study the physico-chemical properties of DNA preparations in solution. As we have seen, by the Hammersten—Bang procedure for preparing relatively highly purified DNA had been established, and Hammersten had shown how the viscosity of DNA preparations changed in the presence of added acid.
Further progress was made by Hollaender and Emmons in [ 32 ]: these researchers had also observed that preparations in water formed a heavy viscous solution, which appeared birefringent under streaming flow.
They also observed ultraviolet radiation-induced depolymerisation of sodium thymonucleate. Despite reservations later expressed by Gulland et al. In , Villbrandt and Tennent [ 27 ] followed up and extended Hammarsten's observations on DNA titrations by using both acid and base and forward and back titrations. Creeth et al. In this way, they were able to explain the anomalous results seen by these and other researchers before.
The data for comparison are shown here in Figure 2. Villbrandt and Tennent were unable to see the effects that Creeth et al. Shortly after the Journal of the Chemical Society publications [ 3 , 20 , 26 ], Creeth's PhD thesis appeared [ 4 ] in which, on page 85, he presented a diagram showing his two-chain model for the structure, interpreted from the viscosity, birefringence and titration results. This model is shown in Figure 3a , alongside the correct Watson—Crick two-chain double-helix model [ 1 ] for comparison Figure 3b.
A putative ball-and-stick model for the Creeth structure constructed by the authors is shown in Figure 4. The backbone nucleotide unit from page 79 , based on his drawing from P. Levene, is shown on the right. Reprinted with permission of J. In both cases, only a small part of the molecule is shown. The Creeth structure from page 85 of his thesis, and shown here as Figure 3a , has two chains and is a long linear molecule with the sugar-phosphate backbone clearly and correctly on the outside of the molecule.
The constituent chains are united down their common length by hydrogen bonding between facing amino and hydroxyl groups of opposite chain bases correctly on the inside of the molecule. All these features are consistent with the correct Watson—Crick structure produced 5 years later.
Creeth's model, although close, falls short on two main grounds:. Creeth also estimated inaccurately the number of hydrogen bonds to be a maximum of two per four phosphorus atoms. Also neither he, nor Gulland or Jordan knew of the equivalence of A with T, and C with G, or of the correct tautomeric keto forms, although Gulland was aware of the work of A. The breaks in the chain were considered consistent with the reduction in viscosity on scission of the hydrogen bonds [ 4 ]:.
The action of acids and alkalis on this model is to sever the hydrogen bonds uniting the individual polynucleotide chains which are thus liberated. Being relatively small and flexible they do not interact to form the network characteristic of the micellar state, and the solution is not very viscous. We now include a retrospective analysis by ourselves of the original Creeth data. Evidence for long linear molecules due to non-Newtonian or shear thinning behaviour of solutions resulting from molecular alignment under shear was clearly seen from both the streaming birefringence and from the effects of hydrostatic pressure on measured relative viscosities: this is evident from Figure 2 similar profiles are given in Figure 3 in ref.
The non-Newtonian effects made it very difficult at the time for Gulland, Creeth or Jordan to comment further on the structure, but with more recent hydrodynamic theory see, for example, ref. Triangles: original solution at 2. Circles: original solution at 0. Squares: solution at 2. As a check we can use a dataset obtained at a lower concentration 0. Finally, also from Figure 4 of ref.
The MHKS relation is. For a rod-shaped molecule, the expected reduction in intrinsic viscosity corresponding to a halving of the molar mass as the two chains come apart would from eqn 3 lead to a maximum reduction of 3. Bearing in mind that the single-chain molecules will be considerably more flexible than their double-chained counterparts — and hence their viscosities will be lower to a certain degree, this plus a halving in molecular mass through hydrogen bond disruption would not be an implausible explanation of the results.
We stress that this is our modern calculation, not a review of Creeth's from his thesis. So, the two-chain hydrogen-bonded model for DNA given in Creeth's PhD thesis could, on the basis of our calculation, have accounted for the viscosity data available at the time and without the need for alternating breaks in the chains. The second scenario — that the action of titrating with acid or alkali could also lead to a fission of intra-chain hydrogen bonds between bases along the same chain — is also consistent with the drop in viscosity and loss of birefringence, and Creeth repeats this in his thesis.
Although the molecular mass would then remain the same, the removal of the bonds could encourage the chain to take a more flexible, less-extended conformation resulting in a lowering of viscosity and loss of birefringence. Besides the breaks, also missing from the Creeth two-chain model is, of course, the double helix and the correct pairing of the bases. Gosling see ref. Florence Bell and W. Astbury did not have access to this high-quality DNA when they published their diffraction images in [ 17 , 18 ].
It is interesting to speculate that if the Nottingham team had made available their high-purity DNA, could the Leeds team have produced images of the same quality as Rosalind Franklin's. In , Gulland and Astbury both attended the same meeting — a meeting of the Society of Experimental Biology in Cambridge, and both contributed to the Proceedings published a year later [ 23 , 34 , 39 ] — this may have been an opportunity lost.
Later, the Leeds team were able to produce a high enough quality image: in , E. Beighton, a researcher in Astbury's laboratory, produced a clear diffraction pattern with the characteristic helical cross see ref. But, by then, it was too late as the Nottingham team had all but gone: Creeth had finished his PhD and had become a research Fellow at the Courtauld Institute in London before moving to the Department of Physical Chemistry in Wisconsin [ 41 ].
His supervisor Doj Jordan moved to take up an appointment at the University of Adelaide, and tragically Masson Gulland was killed in a train crash in October [ 6 ], not long after the publication of the hydrogen bond finding. The Nottingham team also would not have had access to the findings of Chargaff et al. Davidson's classic text [ 42 ] used by Watson. As famously recalled by J. Watson in his book [ 8 ], he and Crick had been struggling to get the T—A and C—G base pairs to fit into the helical structure.
Donohue, a Guggenheim Fellow sharing an office with them at the Cavendish — and an expert on tautometric forms — was able to point out to Watson that Davidson was wrong, and the T and G bases were primarily in the keto form —CO—NH— at physiological pH's [ 8 ]. This enabled Watson and Crick to complete their model, with the bases hydrogen bonded in their correct tautomeric forms Figure 6 , allowing a regular stacking of bases within the antiparallel double helical frame of the sugar-phosphate backbone and at the correct spacing.
The precise hydrogen bond link between the bases made by Watson and Crick followed from the Chargraff base-pair rules and from J. O'Donohue's identification of the correct keto tautomeric form. Adapted with permission from Booth and Hey [ 6 ]. Copyright American Chemical Society. To the modern-day molecular biologist, it is not hard to recognise that the diagram drawn by Creeth [ 4 ] in his PhD thesis Figure 3a bears similarities to sketches that might be drawn today for the design of PCR polymerase chain reaction experiments using multiple annealing primers.
It also resembles current textbook diagrams depicting mechanisms by which some viruses integrate into host chromosomes during their replication cycles using staggered cuts in the duplex and the resulting production of short single-stranded segments e. Stability of doubly and triply H-bonded complexes governed by acidity—basicity relationships. Chemical Communications , 55 11 , The impact on the ring related vibrational frequencies of pyridine of hydrogen bonds with haloforms — a topology perspective.
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Journal of Computational Chemistry , 32 6 , Pallan , Emily M. Nucleic Acids Research , 39 8 , Noncovalent interactions: a challenge for experiment and theory. Chemical Reviews Washington, D. American Chemical Society. A review with refs. The topics discussed include: theor. Infrared spectroscopy of size-selected water and methanol clusters.
After a short description of the exptl. Results are discussed with respect to the relation of spectrum to the structure of the clusters, the role of isomers and their temp. High-resolution ultraviolet spectroscopy of neutral and ionic clusters: hydrogen bonding and the external heavy atom effect.
UV spectroscopy techniques on cluster systems extended from arom. The methods are demonstrated for arom. Rotationally resolved spectroscopy of ionic arom. Elsevier Science B. Y bonds, is discussed. Its universal validity is illustrated over a fold energy range 0. Y hydrogen bonds of different assocs. Interactions and hydration of nucleic acid bases in a vacuum.
Experimental study. A review with 71 refs. Hydrogen-bonded complex formation. Thermodynamics of complexing by infrared spectroscopy and calorimetry. Arnett, Edward M. The formation consts. A 2nd method, the pure base method, which is novel, involves measuring the molar heat of reaction of a small increment of p-fluorophenol in the pure base as solvent where all of the phenol is complexed.
Model compds. Extensive data for heats of soln. These data are used to det. Although the new method is theoretically dubious, agreement with the old method and with reliable values from other labs.
This behavior was also obsd. This contrasts with the behavior of the other types of bases studied. Although the trend is clear, no good general correlation is found. Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition. A review with many refs. The principles of isothermal titrn. Although ITC is particularly suitable to follow the energetics of an assocn. They may be composed to varying degrees of contributions from the binding reaction proper, from conformational changes of the component mols.
Calorimetric determination of hydrogen-bonding enthalpy for neat aliphatic alcohols. Solomonov, Boris N. Hydrogen bonding in pure aliph. For all the studied alcs. A slightly smaller value of From the enthalpies of the specific interactions of the alcs.
The specific interaction and dimerization enthalpies obtained are concurrent with the Badger-Bauer rule and the hydrogen-bond cooperativity effects.
The calorimetric data obtained are supported by literature Fourier transform IR data on dimer and multimer formation for ethanol and octanol in tetrachloromethane soln. Communication: Determination of the bond dissociation energy D0 of the water dimer, H2O 2, by velocity map imaging. Rocher-Casterline, Blithe E. American Institute of Physics. The bond dissocn. The fragments' velocity and center-of-mass translational energy distributions are detd.
An accurate value for D0 is obtained by fitting both the structure in the images and the max. Hydrogen-bond strengths by magnetically induced currents. Royal Society of Chemistry. The authors present a "non-invasive" computational method to est. The method is calibrated using H-bonding dimers, and applied on Watson-Crick DNA base pairs and proton wires in carbonic anhydrase.
Hydrogen Bonding—New Insights , 1 st ed. Atoms in Molecules: A Quantum Theory , 1 st ed. A quantum theory of molecular structure and its applications. A new measure of hydrogen bonding strength - ab initio and atoms in molecules studies. Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities.
We have analyzed the topol. HBs [X-H In spite of different models, methods and exptl. G rCP and the potential energy d. V rCP at the crit. O distance. Moreover, theor. Using the geometric and electron d. NMR shielding consts. O interactions for all the water clusters. The charge transfer interaction in the formation of H-bonds in various water clusters has been assessed with the help of natural bond orbital anal.
A , , — , DOI: Structure, stability, and hydrogen-bonding interaction in phenol, water, and phenol-water clusters have been investigated using ab initio and d.
DFT methods and using various topol. However, fusion of phenol and water clusters leads to stability that is akin to that of H2O clusters.
The presence of hydrogen bond crit. The calcd. Hydrogen bonding in protonated water clusters: an atoms-in-molecules perspective. It is evident from the results that an electron d. Hydrogen bonding without borders: an atoms-in-molecules perspective. The electron d. Electronic structure theory based study of proline interacting with gold nano clusters.
Interaction between metal nanoparticles and biomols. Studies on proline tagged with gold nanoclusters are reported here using d.
The complexes assocd. The electron affinities and vertical ionization potentials for all complexes are calcd. They show an increased value of electron affinity and ionization potential on complexation. Natural bond orbital NBO anal. The results indicate that the nature of interaction between the two moieties is partially covalent. Our results will be useful for further exptl. The Mulliken anal. The results of calcns.
They nucleate base triplets and quartets, participate as loop closing terminal base pairs in hair pin motifs and are also responsible for several tertiary interactions that enable sequentially distant regions to interact with each other in RNA mols.
The BSSE and deformation energy cor. For non protonated base pairs in their optimized geometry, these values ranged from The interaction energies of these base pairs, in their resp. The variation in RMSD between the two geometries was also large and ranged from 0. Our anal. Instead, the nature of local interaction energy hyperspace of different base pairs as inferred from the degree of their resp.
It also suggests that the concept of isostericity alone may not always det. These considerations are more important than the abs. They highlight the importance of revising some of the existing DNA based structure anal. Estimation of individual binding energies in some dimers involving multiple hydrogen bonds using topological properties of electron charge density. Binding to gold nanoclusters alters the hydrogen bonding interactions and electronic properties of canonical and size-expanded DNA base pairs.
RSC Adv. DNA mols. In this work, a comprehensive study to examine the effect of structural perturbations caused to DNA base pairs in terms of size expansion and adsorption on a gold cluster Au3 has been carried out using d. The geometric and electronic features of these complexes provide evidence for the distortion of certain base pairs depending on the binding site of the cluster.
This is further substantiated via normal mode, natural bond orbital NBO and atoms in mols. AIM analyses. The natural population anal. This charge redistribution may offer the possibility of higher order interactions. This study demonstrates the possibility of combining structural modifications to DNA base pairs and subsequent binding to gold nanoparticles to modulate and achieve mol. A theor.
The interaction energy along the dissocn. When this energetic profile is recalcd. Hence, the characteristics of the charged dimers are similar to those of the neutral ones: the addn. The interacting quantum atom IQA method has been used to calc. The IQA results show repulsive electrostatic interactions when the whole mols. B , , — , DOI: It is obsd. Both the QM and MD calcns. Our study clearly reveals that H-bonded water mols. A theoretical study of the infrared spectrum of uracil.
The harmonic frequencies, IR intensities and the potential energy distribution of the vibrational modes of the dioxo tautomer of uracil are calcd. The use of a common scale factor of 0. The use of a potential energy decompn. Molecular structure and vibrational IR spectra of cytosine and its thio and seleno analogues by density functional theory and conventional ab initio calculations. Full geometry optimizations without any constraints on the planarity of the systems were carried out for six tautomers of cytosine and their thio and seleno analogs by means of the d.
At these geometries, the vibrational IR spectra of the tautomers were calcd. Molecular Structure and Infrared Spectra of Adenine. Applying vibrational spectroscopy to the study of nucleobases - adenine as a case-study. New J.
Guanine: a combined study using vibrational spectroscopy and theoretical methods. Spectroscopy , 27 , — , DOI: Lopes, R. Pedro; Marques, M. Paula M. Hindawi Publishing Corp. The present paper reports a conformational study of solid-state anhyd. In both cases, the 7H-keto-amino tautomer was found to be the prevalent form, contrary to aq. This paper is a significant contribution for the existing spectroscopic characterization of this purine base, by unambiguously assigning its vibrational spectra.
QTAIM and vibrational anal. It has been found that for all iHBs with pos. Quantum Chem. DNA base pairs into the Hoogsteen and reverse Hoogsteen forms. Scientific reports , 8 1 , ISSN:. In this study it was theoretically shown that discovered by us recently Brovarets' et al. WC , reverse Watson-Crick.
DNA base pairs are the intermediates of their pairwise. These transitions do not require for their realization the energy-consumable anisotropic rotation of the amino group of A around the exocyclic C6-N6 bond. They are controlled by the non-planar transition states with quasi-orthogonal geometry symmetry C1 joined by the single intermolecular. The Gibbs free energies of activation for these non-dissociative, dipole-active conformational transitions consist 7. Public Library of Science.
In this paper we have theor. QM calcns. Nature of H-bonding in clusters, liquids, and enzymes: an ab initio, natural bond orbital perspective. The extent to which individual H-bonds are helpful in holding the two base pairs together was previously investigated quant.
The method was validated by the detn. Density functional theory DFT and natural bond orbital NBO study of vibrational spectra and intramolecular hydrogen bond interaction of l-ornithine-l-aspartate. Elsevier B. In this study, exhaustive conformations of S aminocarboxybutanaminium S aminocarboxypropanoate LOLA have been scanned. The optimized mol.
The LOLA mol. H-bonds and ionic bonding. Moreover, calcd. Reliable vibrational assignments have been made on the basis of potential energy distribution PED and 0. Hydrogen bonds in complexes of phosphonic and metylphosphonic acids with dimethylformamide. A , 89 , — , DOI: Khatuntseva, E. The structures of the hydrogen-bonded complexes of phosphonic and methylphosphonic acids with DMF were calcd.
The geometrical parameters of hydrogen bonds, intermol. An NBO anal. The obtained values were compared with the corresponding literature data for phosphoric acid complexes. Characterizing the energy of individual intermol. QTAIM theories. Energies of the individual H-bonds, resulting from addn.
The best correlations were found for the NBO energy with the electron d. The correlations held for the heterogeneous samples of HBs of different types, i. Natural hybrid orbitals. From the information contained in the exact or approx. The natural hybrids are optimal in a certain sense, they are efficiently computed, and agree with chem.
Bent's Rule and with hybrids obtained by other procedures. Three examples are given: 1 orbital following during NH3 umbrella inversion, 2 dimerization of water mols. University of Ioannina. A review discusses natural localized bonding concepts, as implemented in the current natural bond orbital program NBO 5. This communication presents quantum mech. Due to the calcd. A new approach to quantify hydrogen bond strengths based on interaction coordinates HBSBIC is proposed and is very promising.
In this research, it is assumed that the projected force field of the fictitious three atoms fragment DHA where D is the proton donor and A is the proton acceptor from the full mol. The "interaction coordinate IC " derived from the internal compliance matrix elements of this three-atom fragment measures how the DH covalent bond its electron d. This response of the DH bond, based on how the IC depends on the electron d. The inter- and intramol.
Because this involves only a three-atom fragment for each hydrogen bond, the approach should open up new directions in the study of "appropriate small fragments" in large biomols. Theoretical investigation of the hydrogen bond strengths in guanine-cytosine and adenine-thymine base pairs. The cooperative contributions to the H-bonding interaction energies of the adenine-thymine and guanine-cytosine base pairs have been evaluated using MO theory.
The energies of the individual bonds in each base pair were ascertained by using models structures that keep one H-bond at a time intact by rotating one base with respect to the other about the axis of each H-bond to form structures with the bases perpendicular to each other. The energies of the individual H-bonds calcd.
The cooperative contributions are of similar magnitude for each base pair. Structural modifications that might strengthen one H-bond tend to weaken another. To the extent that these observations can be generalized, they should be important to the design of materials that utilize H-bonding motifs for self-assembly.
It is widely known that canonical DNA base pairs preserve the Watson-Crick WC scheme of pairing that enables accurate transfer of genetic information across generations. Herein, we firstly present a discovered biol. The estn. These findings significantly expand the horizons of the classical Watson-Crick tautomeric hypothesis of spontaneous point mutagenesis.
Collectively, our investigation revealed the hitherto unknown ability of the canonical Watson-Crick DNA base pairs to switch into the wobble mismatches with mutagenic tautomers, clarifying the nature of genome instability.
Moreover, this paper reveals new facets of the Watson-Crick tautomeric hypothesis of the spontaneous point mutagenesis arising at DNA replication, and significantly broadens the possibilities for the rational design of chem. Most of the diprotonated species studied are stable, even though the binding energy is pos. Local electrostatic attractive forces in the regions of hydrogen bonds HBs are responsible for equil.
Secondary electrostatic effects also affect the assembling of the nucleic acid complexes in either neutral or cationic form. In particular, the elec. Hence, when the nucleophilic site concerns the free lone pair of the heteroatom involved in the HB interaction as acceptor, the HB distance shortens.
However, if the free lone pair of the HB acceptor interacts with an electrophilic site in the same mol. The topol.
Frontiers in genetics , 3 , 59 ISSN:. One of the important goals of most biological investigations is to classify and organize the experimental findings so that they are readily useful for deriving generalized rules.
Although there is a huge amount of information on RNA structures in PDB, there are redundant files, ambiguous synthetic sequences etc. Hence, it would be now a simple assignment to regularly update the classification as and when new structures are released.
The classification can further determine i a non-redundant set of RNA structures and ii if available, a set of structures of identical sequence and function, which can highlight structural polymorphism, ligand-induced conformational alterations etc. Presently, we have classified the available structures PDB entries having RNA chain longer than nine nucleotides solved by X-ray crystallography or NMR spectroscopy into nine functional classes. The structures of same function and same source are mostly seen to be similar with subtle differences depending on their functional complexation.
Density-functional exchange-energy approximation with correct asymptotic behavior.
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