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The idea was that the monomers might associate to form intermolecular complexes that reflect the pairing that occurs in the double helix. The high-resolution diffraction data afforded by single crystals allowed for an objective characterization of hydrogen bonding interactions between the bases. The first such study was reported in , when Karst Hoogsteen — an associate of Robert Corey at Caltech —used single crystal X-ray analysis to determine the structures of co-crystals containing 9-methyladenine and 1-methylthymine, where methyl groups were used to block hydrogen bonding to nitrogen atoms otherwise bonded to sugar carbons in DNA.
As in WC base-pairs, the thymine base formed two hydrogen bonds with the adenine base, one of which thymine O4 and adenine N6 is identical to that proposed by Watson and Crick. However, the second hydrogen bond is not between thymine N3 and adenine N1, but rather, between thymine N3 and N7 of the flipped adenine base Figure 1.
This very same hydrogen bonding scheme was proposed two years earlier by Rich and his colleagues to explain how poly rU strands might associate with poly rA -poly rU duplexes to form triplexes. As predicted earlier by Pauling and his colleagues 12 that G-C base-pairs were stabilized by three and not two hydrogen bonds as proposed by Watson and Crick. However, unlike A-T base-pairs, formation of a second hydrogen bond with N7 of the flipped guanine requires protonation of cytosine N3.
The transition results in a net loss of one hydrogen bond and the build-up of a positive charge on the cytosine. Among the skeptics was Linus Pauling, who had proposed an incorrect triple helix model for the DNA structure the same year that Watson and Crick proposed their double helix model.
Both structures revealed a right-handed double helix with two strands running anti-parallel to each other. Importantly, both structures featured WC type base-pairing. This was the first time a WC rather than HG base-pair was observed involving adenine. The structures seemed to put the controversy regarding HC versus WC A-T base-pairs to rest; since it was the WC form that was favored when the bases were constrained in a double helix.
Six years later, in , following advances in phosphotriester methods for chemical synthesis of large quantities of homogeneous oligonucleotides, 31 , 32 Rich and colleagues reported the first single crystal X-ray structure of DNA for the d CG 3 sequence. As in HG base-pairs, the guanine base is flipped into a syn conformation; however, in Z-DNA, the concomitant flipping of the cytosine base and sugar allows the two flipped bases to regroup into WC base-pairs, with the flipping of the cytosine sugar giving rise to the unusual zig-zag backbone.
Thus, although the first single crystal structure of DNA provided evidence for G-C WC base-pairs, it fueled skepticism about the overall structure of the double helix. In the early s, models were put forward for a Z-DNA structure that are exclusively comprised of HG base-pairs, 35 particularly for A-T rich sequences that frequently exhibited unusual diffraction patterns when dried referred to as D- or E- type X-ray diffraction patterns.
Spectroscopic studies of poly rA -poly rU sequences that bear substituent at the adenine C2 position that sterically block WC base-pairing also suggested formation of duplexes with parallel or anti-parallel chain polarity, in which strands are held together by HG or reverse HG base-pairing, respectively. It is this structure that is considered to be crystallographic proof that DNA can indeed adopt the structure proposed by Watson and Crick.
However, spectroscopic evidence for HG base-pairs continued to mount in the s and s in the context of A-T rich sequences, 41 in poly dG-dC -poly dG-dC sequences at low pH as possible intermediates along the B-to-Z DNA transition, 42 as well as in non-canonical DNA regions as closing base-pairs of apical loops. Together, these features provide a distinct physicochemical presentation of the genetic code for potential sequence-specific recognition by the cellular machinery.
The structure showed that the two quinoxaline rings bis-intercalate in the minor groove of the DNA double helix and surround the WC G-C base-pairs, disrupting stacking interactions to the central A-T base-pairs Figure 3. Remarkably, although the two central A-T base-pairs are not covered by the two triostin A molecules, they form HG rather than the WC base-pairs.
This marked the first crystallographic observation of the co-existence of WC and HG base-pairs within the same duplex. No direct contacts are observed between the antibiotic and the exposed Watson-Crick face of the A-T bases. Rather, the helical constriction at the HG base-pairs appears to stabilize the complex by allowing close packing of the oligonucleotide around the end of the triostin A. Thus, several favorable van der Waals contacts would be lost if the deoxyribose rings were further apart as in WC base-pairs.
Soon after, chemical footprinting studies performed in solution showed that sites that form HG base-pairs in X-ray structures of DNA-echinomycin complexes are hyperreactive to diethyl pyrocarbonate DEPC , 53 which preferentially reacts with exposed N7 atoms of syn purines in non-canonical Z-DNA 54 and cruciform loops.
Subsequent NMR studies by Feigon, Patel, and their co-workers confirmed formation of HG base-pairs in DNA-antibiotic complexes, 60 , 61 although their occurrence was shown to be highly dependent on sequence, temperature, and pH.
These studies raised the possibility that proteins exploit the unique structural and chemical features of HG base-pairs in sequence-specific DNA recognition, and therefore, provided evidence for a functional role for HG base-pairs in vivo. Interestingly, a hydrogen bond was observed between the backbone amide group of an arginine residue and N3 of the syn A, suggesting specific recognition of the Watson-Crick face in the HG base-pair.
However, the nick is involved in crystal packing with a neighboring molecule in the complex and HG formation helps move the phosphate backbone away from a neighboring molecule. In addition, the protein makes specific contacts with N3 of an anti A in a symmetric site in the DNA lacking the nick, suggesting interactions that are specific for WC rather than HG base-pairing.
However, the HG base-pair appears to contribute to binding by preventing steric clashes between the protein leucine 72 and the guanine exocyclic NH2, while still preserving favorable van der Waals contacts with two neighboring phenylalanine residues.
A second G-C HG base-pair was observed but attributed to crystal packing forces. Once again, the HG base-pair appears to avoid unfavorable steric clashes that would otherwise arise with a WC base-pair. The HG base-pair is accommodated within the duplex DNA without inducing major distortions, even for the directly neighboring base-pairs. The ease with which HG base-pairs could seamlessly fit within B-DNA raised the possibility that HG base-pairs may have been incorrectly assigned to be WC base-pairs due to misinterpretation of ambiguous electron density at medium to low resolution.
Remarkably, these HG base-pairs adopt WC conformation in X-ray structures with a longer spacer length 74 or a different intervening sequence 75 , 76 between DNA half-sites, which is accompanied by a different organization between p53 dimers, altered DNA helix conformation, and that also yield different DNA-tetramer binding affinities. Go to: Damaged DNA By the s, it had become clear that DNA could be damaged by exogenous and endogenous factors, and that this in turn may be linked to disease states such as cancer.
The first evidence for HG-type base-pairs in damaged DNA was reported in the late s in solution NMR studies by Patel and co-workers showing that guanine adducts on the Watson-Crick edge or the C8 positions strongly favor a syn base orientation. A The methyl damage green on A N1 causes a steric clash in the WC base-pair, which favors formation of the alternative HG base-pair that relieves the steric clash. There is great speculation and experimental evidence that HG-type pairs play important roles in DNA damage and mismatch repair.
For maximum stability, it was assumed that the double-well-potential is highly asymmetric in DNA duplexes. A large potential barrier is required to reduce the frequency of tautomeric formation and to ensure high purity of DNA replication. The proton tunneling time depends on the form and height of the barrier. Tunneling occurs in both directions through the potential barrier. Reverse tunneling also occurs in two ways either with radiation or through normal proton tunneling.
In the ground state of the AT base pair, the lowest tunneling level has a proton lifetime of 0. The influence of quantum tunneling, which has significant contribution on proton transfer and the reaction pathways Godbeer et al. The conformational and tautomeric composition of monomers of tetrazolyl -acetic acid TAA Araujo-Andrade et al. In a latest study, the hydrogen bonds and its use in molecular recognition were studied by comparing the tunneling-assisted quantum entanglement shared in the ground states of covalent and hydrogen bonds Pusuluk et al.
It was seen that there is significant amounts of quantum entanglement for the thermal state of hydrogen bond. The density-functional theory calculations with hybrid functionals and van der Waals corrections, and optimized path-integral ring-polymer methods Litman et al.
The results indicated that below K, the concerted double hydrogen transfer DHT tunneling pathway dominates, while including the nuclear quantum effects for and K, the concerted and stepwise pathways are selected. Further, the researchers provided architecture for the physical understanding of hydrogen transfer dynamics in the complex systems. Repeated transitions revert back to their original structures.
In these mutations, the DNA strand turns either into junk DNA and thus fails to pass on its encoded information and directions, or turns into malfunctioned DNA to give destructive information. In the twentieth century, quantum-mechanical studies were carried out to predict the tautomeric equilibria of heterocyclic compounds. Few parameters such as ultraviolet spectra, dipole moments, and ionization potentials were calculated using semi-empirical or non-empirical quantum-mechanical computational method as per the requirements.
These calculations were found to be useful to predict the relative stability of the tautomers in vapor phase in solution and the influence of substituents Kwiatkowski et al. The change in tautomeric equilibria of DNA bases that occurs due to the changes from an inert to a polar environment was discussed in a review with the extensive work of the past 14 years Person et al. The tautomeric equilibria of 2 4 -mono oxopyrimidines in the gas phase and solution were studied at low-temperature matrices Nowak et al.
Energies, heats of vaporization, and UV spectra were calculated and compared to the known experimental data. A study on potential energy surface PES of guanine performed by Prof. Leszczynski's group showed that the PES of guanine is not flat. The basic feature of this model was the study of tautomerization in the biological environment of duplex DNA. Further, it was seen that the biochemical knowledge on biosynthesis of nucleotides, DNA and RNA sequence information and transmission, interaction of nucleic acids with proteins, and DNA sequence rearrangements and alterations are the most important things Blackburn and Gait, Computational studies about the tautomerism and protonation of guanine and cytosine in the gas phase and in aqueous solution were carried out for the most stable tautomeric forms of the neutral and protonated nucleic acid bases Colominas et al.
The results indicated the H-bonded structure of the cytosine dimer to be more stable than the stacked structures of these pairs. Similarly, the double-proton transfer in adenine—thymine AT and GC base pairs in gas phase Gorb et al.
The results revealed that the hydrogen-bonded bases possess non-planar geometries. The calculations predicted greater stability for canonic or rare forms of the DNA bases occurring in water molecules and metal cations. Several other computational studies were also carried out for the nucleobases Hobza, ; Stewart et al.
The intramolecular proton transfer in mono- and dihydrated tautomers of guanine Gorb and Leszczynski, ; Gorb et al. It was found that the two-fold water influences the NH2-non-planarity phenomena and decreases the non-planarity for the oxo-tautomers.
The two-fold water is the source of non-planarity for the hydroxo tautomers and it decreases the non-planarity for the oxo tautomers. It was concluded that the driven wave packet is dependent on the parameters of the model Hamiltonian and the propagation time. The stepwise mechanism was dominated in most of the cases, while concerted transfer via tunneling occurs for high barrier systems. The field of proton transfer in hydrogen-bonded networks was also explained in the review by Marx The review gave insights into Grotthuss diffusion in water, excited-state proton transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin with the ab initio simulation techniques.
Computational calculations on the hydrogen atom transfer in the cytosine—guanine base pair Villani, and its coupling with electronic rearrangement were studied. It was observed that a different behavior occurred when the hydrogen transfer begins with a H of the guanine or of the cytosine and concerted synchronic in the N—N and asynchronic in the N—O double-hydrogen transfer can be activated only when the first H atom of guanine is moved.
The concerted double-hydrogen process begins with the hydrogen atom of a purinic base. Ab initio constrained molecular dynamics and metadynamics were used to study the mechanism of proton transfer in DNA base pairs AT, GC in the gas phase at room temperature Xiao et al. Interestingly, the results reveal the DPT in the GC base pair to be a concerted and asynchronous mechanism and in AT to be a stepwise and an asynchronous mechanism.
The double-proton transfer reactions in WC GC base pairs were studied after the addition of hydrogen atom Lin et al. The results revealed that the concerted double-proton transfer mechanism is favorable in the gas phase and the stepwise mechanism is favorable in water with the PT products being energetically less favored.
Oxidized nucleobases removal of one valence electron also exhibit enhanced acidity, which leads to PT between the strands of DNA Ghosh and Schuster, and competes with the migration of electron hole along the strands Charkaborty, The experimental and electronic structure calculations Khistyaev et al. The barrierless H-bonded pairs in ionization-induced species predict higher efficiency for the process. At this stage, the energy level of proton is equal for the reactants and products Li et al.
Water is considered as a very important complex in the PT biological systems Ball, For example, water filled ion channels through interfaces and membranes and in aerosols Voth, A relay-type transport of protons is provided by water wires, which is important for all processes Agmon, ; Chandler et al. Water wires are involved in the proton-coupled electron transfer in DNA. The excited state photo acid structures Mohammed et al. The experimental and energetic calculations on dimethyluracil dimers predict superficial proton transfer in the absence of hydrogen bonds Golan et al.
Experiments were carried out to investigate the nature and dynamics of proton transfer in stacked systems and molecular dynamics calculations were carried out to visualize the actual proton transfer mechanism. See Figure 5. The results reveal strong silver—WC pair's interaction and absorption in the visible region.
Similarly, theoretical studies on the electronic and optoelectronic properties of [A. After analyzing the different parameters, the results indicated the applicability of these complexes in fluorescent bioimaging. Optimized structures of [A.
Studies have been carried out to find the relationship between charge transport and proton transfer. The effect of water molecules led to proton transfer for the cationic stack of AT while a pKa experiment does not predict proton transfer in AT base pairs Steenken, ; Colson et al. A recent study reported that proton transfer occurs at high temperature as well. Here, two different mechanisms displacement and oriental polarization were proposed for the CT and PT at different degrees of temperatures Zengtao et al.
It was observed that multiple proton transfer occurred at low temperatures and the water-assisted PT occurred by displacement polarization and oriented polarization mechanisms. The rate of PT decreased at higher temperature with water shifting the polarization mode to enhance the PT rate.
Further, it was concluded that higher temperature lowers the probability of proton transfer and PT is favored at low temperatures. Suggested mechanisms by arrows for double proton transfer in hydrated 1 AT and 2 GC base pairs. The results for the series of nucleobase complexes with organic or inorganic proton donors indicated that electron attachment to these complexes in the gas phase induces PT, which leads to the strong stability for the valence anions Dabkowska et al.
The probability of stable anion formation in the surrounding of DNA complexes was also studied. The intermolecular PT to excess electron attachment of adenine—formic acid hydrogen-bonded complexes indicated more involvement of adenine bases in proton-donor and -acceptor centers and hydrogen-bonding interactions Mazurkiewicz et al. Further, it was predicted that the stability of the valence ion will increase with the involvement of more species with the nucleobases.
As the large affinities of adenine complexes are counter balanced by many physiological environmental factors, they play an important role in the induced mutations by low energy electrons. Studies have been conducted for the selectively modified DNA structures, which show promising applications for ultrashort electric pulses in medicine. An analytical review on two-dimensional 2D potential-energy surface based on two equal hydrogen bonds coupled by a correlation term was given to describe the dynamics of the DPT mechanism Smedarchina et al.
The work has been carried out for the dominant role of tunneling in condensed phases and at high temperatures for DHT in porphycenes by experimental means. In these studies, the mutations were energetically favorable for GC pairs. The tautomeric equilibria of isolated WC base pairs in gas phase and solvent phase Gorb et al.
The accurate theoretical predictions for biological activities were given with the proposed chemical models. Structural representation of the single and double proton transfer mechanisms of canonical AT, GC pairs. Catalyzing the spontaneous mutation increases the proton acceptance and donation with DNA.
The SPT zwitterionic product acts as a transient species, and the shift of equilibrium to the canonical form occurred for the direct and water-assisted mechanism in AT base pair. Liang and co-workers used the molecular dynamics MD method to study the motions of proton Xiao et al. PT reactions in DNA can be altered by metals and free radicals or the high-energy radiation and electric field.
Though the genotoxic agents create a damaging role in spontaneous mutations, its influence in cancer cells can be positively controlled Xiao et al. A novel approach for the internal treatment of cancer with the action of an external physical agent with chemotherapeutic drug was suggested, which controls the exposure region and time duration.
The intramolecular PT reactions were studied for both isolated and hydrated DNA bases, while the intermolecular SP and DP transfer reactions are seen in the nucleic acid bases dimers at both ground and excited electronic states Sekiya and Sakota, Small activation barriers were seen for GC anionic and cationic pairs. The tautomeric equilibria and kinetic parameters lifetime and rate constants were defined by the activation barrier Atkins, Further, it was studied that the PT reaction is more favorable for the anion as compared to the cation.
In the uracil and alanine interactions, the results demonstrated the possibility of electron-induced mutations in DNA—protein complexes. The effect of polarity was also studied for the dipole-bound anionic states. DNA replication errors that are caused by genomic instability Liu et al.
The high-energy tautomerized states Brovarets' and Hovorun, , f and wobble pairs Brovarets' and Hovorun, b for the mutagenic tautomerization of canonical base pairs were studied by Prof. Brovarets et al. The tautomerization occurred via the sequential intrapair proton transfer and shifted to the related pairs Brovarets' and Hovorun, b.
The studies were followed by other similar studies Brovarets' and Hovorun, , b , c , d , by the same group. Interestingly, the proton transfer reactions for cytosine-specific DNA-binding proteins for cytosine and 5-fluorocytosine with 5-nitrouracil, CytNit, and 5FcytNit were also studied Portalone, For the unusual combination of NABs pair, normal hydrogen-bonding pattern in DNA is altered, which leads to spontaneous mutations.
The SPT products for base pairs are largely stabilized due to the transfer of a positive charge.
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