带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

The catalytic power of uracil DNA glycosylase in the opening of thymine base pairs

Uracil DNA glycosylase (UNG) locates uracil and its structural congener thymine in the context of duplex DNA using a base flipping mechanism. NMR imino proton exchange measurements were performed on free and UNG-bound DNA duplexes in which a single thymine (T) was paired with a series of adenine analogues (X) capable of forming one, two, or three hydrogen bonds. The base pair opening equilibrium for the free DNA increased 55-fold as the number of hydrogen bonds decreased, but the opening rate constants were nearly the same in the absence and presence of UNG. In contrast, UNG was found to slow the base pair closing rate constants (kcl) compared to each free duplex by a factor of 3- to 23-fold. These findings indicate that regardless of the inherent thermodynamic stability of the TX pair, UNG does not alter the spontaneous opening rate. Instead, the enzyme holds the spontaneously expelled thymine (or uracil) in a transient extrahelical sieving site where it may partition forward into the enzyme active site (uracil) or back into the DNA base stack (thymine).     

Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex

Results obtained using 2,4-difluorotoluene nucleobase (dF) as a nonpolar thymine isostere by Kool and colleagues challenged the Watson-Crick dogma that hydrogen bonds between complementary bases are an absolute requirement for accurate DNA replication. Here, we report crystal structure of an RB69 DNA polymerase L561A/S565G/Y567A triple mutant ternary complex with a templating dF opposite dTTP at 1.8 ?-resolution. In this structure, direct hydrogen bonds were observed between: (i) dF and the incoming dTTP, (ii) dF and residue G568 of the polymerase, and (iii) dF and ordered water molecules surrounding the nascent base pair. Therefore, this structure provides evidence that a templating dF can form novel hydrogen bonds with the incoming dTTP and with the enzyme that differ from those formed with a templating dT.     

Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

The physical and chemical factors that allow DNA to perform its functions in the cell have been studied for several decades. Recent advances in the synthesis and manipulation of DNA have allowed this field to move ahead especially rapidly during the past fifteen years. One of the most common chemical approaches to the study of interactions involving DNA has been the use of DNA base analogues in which functional groups are added, deleted, blocked, or rearranged. Here we describe a different strategy, in which the polar natural DNA bases are replaced by nonpolar aromatic molecules of the same size and shape. This allows the evaluation of polar interactions (such as hydrogen bonding) with little or no interference from steric effects. We have used these nonpolar nucleoside isosteres as probes of noncovalent interactions such as DNA base pairing and protein - DNA recognition. We have found that, while base-pairing selectivity does depend on Watson - Crick hydrogen bonding in the natural pairs, it is possible to design new bases that pair selectively and stably in the absence of hydrogen bonds. In addition, studies have been carried out with DNA polymerase enzymes to investigate the importance of Watson - Crick hydrogen bonding in enzymatic DNA replication. Surprisingly, this hydrogen bonding is not necessary for efficient enzymatic synthesis of a base pair, and significant levels of selectivity can arise from steric effects alone. These results may have significant impact both on the study of basic biomolecular interactions and in the design of new, functionally active biomolecules.     

Halogen bonding in DNA base pairs

Halogen bonding (R-X···Y) is a qualitative analogue of hydrogen bonding that may prove useful in the rational design of artificial proteins and nucleotides. We explore halogen-bonded DNA base pairs containing modified guanine, cytosine, adenine and thymine nucleosides. The structures and stabilities of the halogenated systems are compared to the normal hydrogen bonded base pairs. In most cases, energetically stable, coplanar structures are identified. In the most favorable cases, halogenated base pair stabilities are within 2 kcal mol(-1) of the hydrogen bonded analogues. Among the halogens X = Cl, Br, and I, bromine is best suited for inclusion in these biological systems because it possesses the best combination of polarizability and steric suitability. We find that the most stable structures result from a single substitution of a hydrogen bond for a halogen bond in dA:dT and dG:dC base pairs, which allows 1 or 2 hydrogen bonds, respectively, to complement the halogen bond.     

DNA sequencing with titanium nitride electrodes

We construct a hydrogen‐bond based metal–molecule–metal junction, which contains two identical “reader” molecules, one single DNA base as a bridged molecule, and two titanium nitride electrodes. Hydrogen bonds are formed between “reader” molecules and DNA base, whereas titanium–sulfur bonds are formed between “reader” molecules and titanium nitride electrodes. We perform electronic structure calculations for both the bare bridged molecule and the full metal–molecule–metal system. The projected density of states shows that when the molecule is connected to the titanium nitride electrode, the energy levels of the bridged molecule are shifted, with an indirect effect on the hydrogen bonds. This is similar to the case for a gold electrode but with a more pronounced effect. We also calculate the current–voltage characteristics for the molecular junctions containing each DNA base. Results show that titanium nitride as an electrode can generate distinct conductance for each DNA base, providing an alternative electrode for DNA sequencing. © 2013 Wiley Periodicals, Inc.     

Use of molecular analogs for the bases in DNA: Stability of molecular pairs in gas phase and aqueous media and possible role of hydrogen bonding

In a recent experimental study, it was reported that replacement of thymine in the adenine–thymine base pair of DNA by its molecular analogs which cannot form proper hydrogen bonds with adenine (A) does not cause disruption of DNA structure and synthesis. AM1 and ab initio molecular orbital calculations and electric field mapping were carried out in order to examine the possibility of pairing of A with each one of two analogs of thymine in the gas phase. Self-consistent reaction field calculations were also carried out on the individual molecules and their pairs using the polarized continuum model in order to examine their stability in aqueous media. Our results are broadly in agreement with the conclusions drawn in the above-mentioned experimental work. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 68: 351–355, 1998     

Fluorous base-pairing effects in a DNA polymerase active site

We describe selective "fluorous" effects in the active site of a DNA polymerase, by using nucleotide analogues whose pairing edges are perfluorinated. The 5'-triphosphate deoxynucleotide derivatives of DNA base analogues 2,3,4,5-tetrafluorobenzene ((F)B) and 4,5,6,7-tetrafluoroindole ((F)I), as well as hydrocarbon controls benzene (B) and indole (I), were synthesized and studied as substrates for the DNA Polymerase I Klenow fragment (KF exo-). Modified nucleotides were present in the DNA template or were supplied as nucleoside triphosphates in studies of the steady-state kinetics of single nucleotide insertion. When supplied opposite the non-natural bases in the template strand, the hydrophobic nucleoside triphosphates were incorporated by up to two orders of magnitude more efficiently than the natural deoxynucleoside triphosphates. The purine-like fluorinated indole nucleotide ((F)I) was the most efficiently inserted of the four hydrophobic analogues, with the most effective incorporation occurring opposite the pyrimidine-like tetrafluorobenzene ((F)B). In all cases, the polyfluorinated base pairs were more efficiently processed than the analogous hydrocarbon pairs. A preliminary test of polymerase extension beyond these pairs showed that only the (F)B base is appreciably extended; the inefficient extension is consistent with recently published data regarding other nonpolar base pairs. These results suggest the importance of hydrophobicity, stacking, and steric interactions in the polymerase-mediated replication of DNA base pairs that lack hydrogen bonds. These findings further suggest that the enhanced hydrophobicity of polyfluoroaromatic bases could be employed in the design of new, selective base pairs that are orthogonal to the natural Watson-Crick pairs used in replication.     

Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.     

Selective product amplification of thymine photodimer by recognition-directed supramolecular assistance

Two symmetric ditopic supramolecular templates (1 and 2) each presenting two hydrogen bonding recognition subunits were synthesized. Each such subunit comprises the same donor and acceptor pattern, capable of binding a substrate molecule with complementary hydrogen bonding groups to form a supramolecular complex. Substrate molecules, such as thymine or uracil derivatives, yield 2 : 1 complexes with the acceptors involving two hydrogen bonds to each subunit with ideal orientation for subsequent [2 + 2] dimerization upon photoirradiation. Selective syn photoproduct formation and concomitant suppression of the trans isomer are favored by orientation of the two guest nucleobases within the template cleft. Complementary donor and acceptor hydrogen bonding induced positioning of the two substrates and steric hindrance within the template clefts are responsible for the selective product formation.     

Hydrogen bonds of RNA are stronger than those of DNA, but NMR monitors only presence of methyl substituent in uracil/thymine

Recently, Vakonakis and LiWang (J. Am. Chem. Soc. 2004, 126, 5688) reported experimental evidence for stronger hydrogen bonds in RNA A:U than in DNA A:T base pairs, which was based on differences in NMR shielding for adenine C2. We have analyzed the proposed correlation between NMR shielding and hydrogen-bond strength using density functional theory. Although we agree with the conclusion that A:U is more strongly bound, we find no correlation between the hydrogen-bond strength and the NMR shielding of C2. Our study shows that NMR merely probes the presence/absence of the methyl group in thymine/uracil, without any relation to the strength of the hydrogen bonds involved. In other words, one cannot infer the Watson-Crick hydrogen-bond strength from the NMR shielding constant of adenine C2.     

Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesion

One nanosecond molecular dynamics (MD) simulation of a thymine glycol (TG)-lesioned part of human lymphoblast AG9387 was performed to determine structural changes in DNA molecule caused by the presence of a lesion. These changes can be significant for proper recognition of lesions by a repair enzyme. Thymine glycol is the DNA oxidative lesion formed by addition of OH radicals to C5 and C6 atoms of the thymine base. This lesion is known as causing Cockayne Syndrome-inherited genetic disorder. Distribution of water molecules in a hydration shell around the DNA molecule was analyzed for its contribution to the recognition of the TG lesion by the repair enzyme. The results of MD simulation show there is a specific DNA structural configuration formed at the lesion. After 500 ps the DNA is bent in a kink at the TG site. This change dislocates the glycosyl bond at C5' to a position closer to the DNA surface, and thus its atoms are more exposed to the surrounding water shell. The increased number of water molecules that are close to the TG site indicates that the glycosyl bond may be easily contacted by the repair enzyme. In addition, the higher number of water molecules at the TG site substantiates the importance of water-mediated hydrogen bonds created between the repair enzyme and the DNA upon formation of the complex. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1723-1731, 2001     

Hydrogen-abstracted adenine-thymine radicals with interesting transferable properties

The formation of radicals on DNA bases through various pathways can lead to harmful structural alterations. Such processes are of interest for preventing alteration of healthy DNA and, conversely, to develop more refined methods for inhibiting the replication of unwanted mutagenic DNA. In the present work, we explore theoretically the energetic and structural properties of the nine possible neutral radicals formed via hydrogen abstraction from the adenine-thymine base pair. The lowest energy radical is formed by loss of a hydrogen atom from the methyl group of thymine. The next lowest energy radicals, lying 8 and 9 kcal mol-1 higher than the global minimum, are those in which hydrogens are removed from the two nitrogens that would join the base pair to 2-deoxyribose in double-stranded DNA. The other six radicals lie between 16 and 32 kcal mol-1 higher in energy. Unlike the guanine-cytosine base pair, adenine-thymine (A-T) exhibits only minor structural changes upon hydrogen abstraction, with all A-T derived radicals maintaining planarity. Moreover, the energetic ordering for the radicals of the two isolated bases (adenine and thymine) is preserved upon formation of the base pair, though with a wider spread of energies. Even more significantly, the energetic interleaving of the (A-H)*-T and A-(T-H)* radicals is correctly predicted from the X-H bond dissociation energies of the isolated adenine and thymine. This suggests that the addition of the hydrogen-bonded complement base only marginally affects the bond energies.     

Theoretical studies on interactions between low energy electrons and protein-DNA fragments: valence anions of AT-amino acids side chain complexes

Electron attachment to trimeric complexes that mimic most frequent hydrogen bonding interactions between an amino acid side chain (AASC) and the Watson-Crick (WC) 9-methyladenine-1-methylthymine (MAMT) base pair has been studied at the B3LYP/6-31++G(d,p) level of theory. Although the neutral trimers will not occur in the gas phase due to unfavorable free energy of stabilization (G(stab)) they should form a protein-DNA complex where entropy changes related to formation of such a complex will more than balance its disadvantageous G(stab). The most stable neutrals possess an identical pattern of hydrogen bonds (HBs). In addition, the proton-acceptor (N7) and proton-donor (N10) atoms of adenine involved in those HBs are located in the main groove of DNA. All neutral structures support the adiabatically stable valence anions in which the excess electron is localized on a π* orbital of thymine. The vertical detachment energies (VDEs) of anions corresponding to the most stable neutrals are substantially smaller than that of the isolated WC MAMT base pair. Hence, electron transfer from the anionic thymine to the phosphate group and as a consequence formation of a single strand break (SSB) should proceed more efficiently in a protein-dsDNA complex than in the naked dsDNA as far as electron attachment to thymine is concerned.     

Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

The oligonucleotide d(TX)₉, which consists of an octadecamer sequence with alternating non‐canonical 7‐deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double‐stranded DNA through the formation of hydrogen‐bonded Watson–Crick base pairs. dsDNA with metal‐mediated base pairs was then obtained by selectively replacing W‐C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag⁺ ions, and its stability is significantly enhanced in the presence of Ag⁺ ions while its double‐helix structure is retained. Temperature‐dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)‐mediated base pairs. This strategy could become useful for preparing stable metallo‐DNA‐based nanostructures.     

A series of nonpolar thymidine analogues of increasing size: DNA base pairing and stacking properties

[reaction: see text] We describe the properties in DNA of a set of five nonpolar nucleoside mimics in which shape is similar but size is increased gradually. The compounds vary in the size of their exocyclic substituents, which range from hydrogen to iodine, and are designed to test the steric effects of nucleosides, nucleotides, and DNA in biological systems in a systematic way. We describe the conversion of toluene, 2,4-difluorotoluene, 2,4-dichlorotoluene, 2,4-dibromotoluene, and 2,4-diiodotoluene deoxyribosides into suitably protected phosphoramidite derivatives and their incorporation into synthetic DNAs. Studies of their behavior in the context of hexamer and dodecamer duplexes were carried out, with comparison to natural thymine. Thermal melting data with compounds in 5' dangling positions showed that all five compounds stack more strongly than thymine, and all the dihalo-substituted cases stack more strongly than the unsubstituted toluene case. Stacking correlated with surface area and hydrophobicity, both of which increase across the series. In base-pairing studies, all five compounds showed destabilized pairing opposite natural bases (relative to thymine-adenine pairing), as expected. Notably, pairing among the nonpolar base analogues was considerably more stable, and some of the pairs involving the largest analogues showed stability equal to that of a natural thymine-adenine pair. The results establish the base pairing properties of a potentially useful new series of biochemical probes for DNA-protein interactions and also identify a set of new, stable hydrophobic base pairs for designed genetic pairing systems.     

Single Crystals of Poly(phenyl glycidyl ether)

Abstract

The Watson-Crick model for DNA has been modified to account for observed physical phenomena associated with DNA. The viscosity data obtained on both partially denatured DNA and on undenatured DNA in various aqueous salt solutions give rise to acidic-type cationic sequences. These results can only be explained if there exist additional bonds other than the hydrogen bonds between base pairs. Considering the experimental data, the only possible type of bond that could exist is an ionic bond between the negatively charged phosphate group and the polar or positively charged nitrogen atom attached to the C'-1 position of the deoxyribose unit. The formation of such an ionic bond produces a natural twist in the DNA strand. The model is also applicable to RNA, although steric factors affect the stability and structure of such an RNA. Values of ΔH for the formation of the DNA and RNA double helix substantiate the proposed models. The most plausible structure for the double-stranded DNA helix is a model where the base pairs are on the surface rather than on the interior of the helix. Hydrophobic bonds do not exist except possibly in the altered structure produced during preparation of the DNA for X-ray analyses. The viscosity results on undenatured DNA in various salt solutions are caused by two factors: a destruction of the ionic bond and a reversal of charge effect on the DNA. The results show that the charge on DNA must change from a negative to a positive charge with addition of salt. The proposed model is applied to replication of DNA and formation of RNA from DNA and associated phenomena.     

The shape of the potential energy curves for NHN(+) hydrogen bonds and the influence of non-linearity

The potential energy curves for proton motion in NHN(+) hydrogen bonds have been calculated to investigate whether different methods of evaluation give different results: for linear H bonds most curves calculated along the NH direction are, as expected, identical with those along NN; for intramolecular H bonds it is very important to take into account the non-linearity and the potential energy curve calculated along the NH direction can be very far from the curve correctly describing the proton transfer. Other factors which influence the proton-transfer process are steric hindrance and presence of anions which modify the proton motion. In the analysis of the proton transfer process it is very important to take changes in the structure of the rest of the molecule into account, which is connected with exchange of energy with the surroundings. Comparison of adiabatic and non-adiabatic curves shows that they are significantly different for very bent hydrogen bonds and for hydrogen bonds with steric constraints for which the proton transfer process must be accompanied with relaxation of the whole molecule. Comparison of the potential-energy curves for compounds with very short H bonds emphasizes that the term 'strong H bond' needs to be qualified. For intermolecular H bonds shortening of the bond is connected with linearization. But for intramolecular H bonds the NN distance cannot be used as the only measure of H bond strength.