Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-watson-crick/sugar edge base pair family

The structure and function of RNA molecules are substantially affected by non-Watson-Crick base pairs actively utilizing the 2'-hydroxyl group of ribose. Here we correlate scalar coupling constants across the noncovalent contacts calculated for the cis- and trans-WC/SE (Watson-Crick/sugar edge) RNA base pairs with the geometry of base to base and sugar to base hydrogen bond(s). 23 RNA base pairs from the 32 investigated were found in RNA crystal structures, and the calculated scalar couplings are therefore experimentally relevant with regard to the binding patterns occurring in this class of RNA base pairs. The intermolecular scalar couplings 1hJ(N,H), 2hJ(N,N), 2hJ(C,H), and 3hJ(C,N) were calculated for the N-H...N and N-H...O=C base to base contacts and various noncovalent links between the sugar hydroxyl and RNA base. Also, the intramolecular 1J(N,H) and 2J(C,H) couplings were calculated for the amino or imino group of RNA base and the ribose 2'-hydroxyl group involved in the noncovalent interactions. The calculated scalar couplings have implications for validation of local geometry, show specificity for the amino and imino groups of RNA base involved in the linkage, and can be used for discrimination between the cis- and trans-WC/SE base pairs. The RNA base pairs within an isosteric subclass of the WC/SE binding patterns can be further sorted according to the scalar couplings calculated across different local noncovalent contacts. The effect of explicit water inserted in the RNA base pairs on the magnitude of the scalar couplings was calculated, and the data for discrimination between the water-inserted and direct RNA base pairs are presented. The calculated NMR data are significant for structural interpretation of the scalar couplings in the noncanonical RNA base pairs.     

Factors determining the deriving force of DNA formation: geometrical differences of base pairs, dehydration of bases, and the arginine assisting

The mechanism of the fidelity synthesis of DNA associated with the process of dGTP combination to the DNA template was explored. The exclusion of water molecules from the hydrated DNA bases can amplify the energy difference between the correct and incorrect base pairs, but the effect of the water molecules on the Gibbs free energy of formation is dependent on the binding sites for the water molecules. The water detachment from the incoming dNTP is not the only factor but the first step for the successful replication of DNA. The second step is the selection of the DNA polymerase on the DNA base pair through the comparison between the correct DNA base and the incorrect DNA base. The bonding of the Arg668 with the incoming dNTP can enlarge the Gibbs free energies of formation of the base pairs, especially the correct base pairs, thus increasing the driving force of DNA formation. When the DNA base of the primer terminus is correct, the extension of the guanine and the adenine is quicker than that of the cytosine and the thymine because of the hydrogen bonding fork formation of Arg668 with the minor groove of the primer terminus and the ring oxygen of the deoxyribose moiety of the incoming dNTP. Because of the geometry differences of the incorrect base pairs with the correct base pairs, the effect from the DNA polymerase is smaller on the incorrect base pair than on the correct base pair, and the extension of a mispair is slower than that of a correct base pair. This decreases the extension rate of the base pair and thus allows proofreading exonuclease activity to excise the incorrect base pair. Arg668 cannot prevent the extension of the GT mispair, as well as the GC correct base pair, and GA and GG mispairs. This may be attributed to the small geometry difference between the GT base pair and the correct AT base pair.     

固体碱催化剂

综述了最近30年来固体碱催化剂的研究现状，包括固体碱催化剂的种类、优缺点以及各类催化剂中影响其催化性能的因素。重点探讨了碱性前驱体和载体对负载型无机固化碱碱强度的影响，展望了未来固体碱剂的发展方向。     

Structures for controlling synthesis design and reaction modelling via knowledge acquisition

The performance of programs for computer-assisted organic synthesis (CAOS) is directly related to the knowledge base and to the procedures for deciding how the knowledge base should be used. The architecture of a knowledge base (text base, data base, rule base, model base and commonsense base) is discussed. The problem of knowledge acquisition is described with regard to pruning the productivity of CAOS systems. The commercial program 1stCLASS (for symbolic processing) is used with the SAAO (devised here for numeric processing) to form a commonsense base. For this purpose, knowledge was acquired by induction from the solutions provided by human experts to given problems. The general procedure is applied to the recognition of reaction sites which are crucial in the simulation of organic reactions.     

Sequence dependence in base flipping: experimental and computational studies

Base flipping is the movement of a DNA base from an intrahelical, base-stacked position to an extrahelical, solvent-exposed position. As there are favorable interactions for an intrahelical base, both hydrogen bonding and base stacking, base flipping is expected to be energetically prohibitive for an undamaged DNA duplex. For damaged DNA bases, however, the energetic cost of base flipping may be considerably lower. Using a selective, non-covalent assay for base flipping, the sequence dependence of base flipping in DNA sequences containing an abasic site has been studied. The dissociation constants of the zinc-cyclen complex to small molecules and single strands of DNA as well as the equilibrium constants for base flipping have been determined for these sequences. Molecular dynamics simulations of the zinc-cyclen complex bound to both single- and double-stranded DNA have been performed in an attempt to rationalize the differences in the dissociation constants obtained for the two systems. The results are compared to previous studies of base flipping in DNA containing an abasic site.     

钙基负载型固体碱催化酯交换反应活性评价

动植物油脂与醇通过酯交换反应制备生物柴油,目前,工业上一般采用NaOH、KOH、NaOCH,等均相催化剂。均相催化剂的缺点是产品后处理复杂,产生大量含碱含油工业废水。而非均相固体碱催化酯交换反应,产品与催化剂分离容易,产品不需要水洗,避免了大量废液的排放。采用非均相固体碱制备生物柴油的文献报道较多,但固体碱的碱中心数、碱中心强度对酯交换反应影响的报道较少。本研究制备了钙基负载型固体碱催化剂,重点研究钙基负载型固体碱的制备工艺条件对碱强度、碱量分布的影响,考察碱强度、碱量分布对催化菜籽油与甲醇的酯交换反应制备生物柴油转化率的影响。     

Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies

The importance of non-Watson-Crick base pairs in the three-dimensional structure of RNA is now well established. The structure and stability of these noncanonical base pairs are, however, poorly understood. We have attempted to understand structural features of 33 frequently occurring base pairs using density functional theory. These are of three types, namely (i) those stabilized by two or more polar hydrogen bonds between the bases, (ii) those having one polar and another C-H...O/N type interactions, and (iii) those having one H-bond between the bases and another involving one of the sugars linked to the bases. We found that the base pairs having two polar H-bonds are very stable as compared to those having one C-H...O/N interaction. Our quantitatively analysis of structures of these optimized base pairs indicates that they possess a different amount of nonplanarity with large propeller or buckle values as also observed in the crystal structures. We further found that geometry optimization does not modify the hydrogen-bonding pattern, as values of shear and open angle of the base pairs remain conserved. The structures of initial crystal geometry and final optimized geometry of some base pairs having only one polar H-bond and a C-H...O/N interaction, however, are significantly different, indicating the weak nature of the nonpolar interaction. The base pair flexibility, as measured from normal-mode analysis, in terms of the intrinsic standard deviations of the base pair structural parameters are in conformity with those calculated from RNA crystal structures. We also noticed that deformation of a base pair along the stretch direction is impossible for all of the base pairs, and movements of the base pairs along shear and open are also quite restricted. The base pair opening mode through alteration of propeller or buckle is considerably less restricted for most of the base pairs.     

Mixed base of hydrophilic ointment and purified lanolin to improve the drug release rate and absorption of water of minocycline hydrochloride ointment for treatment of bedsores.

A desired ointment bases for better treatment of bedsores was developed to improve the release rate of minocycline hydrochloride (MH) and the water absorption capacity using various types of hydrophobic to hydrophilic ointment base. The influence of purified lanolin (PL) on the release behavior of MH from hydrophilic ointment (HO) base was primarily focused on. It was found that the release rate of drug increased with increase in the hydrophilicity of the base. A linear correlation between the apparent release rate constant of drug from the HO and PL mixed ointment base at various combination ratios and the elution of ointment base was noted. The HO ointment base containing 30% PL had the highest apparent release rate constant of MH. The mixed ointment base with the lowest viscosity showed the highest absorption of water and elution of ointment base. In conclusion, it was found that HO (70%) and PL (30%) mixed ointment base was a promising candidate for better treatment of bedsores.     

Hg(II) ion specifically binds with T:T mismatched base pair in duplex DNA

Metal-mediated base pair formation, resulting from the interaction between metal ions and artificial bases in oligonucleotides, has been developed for its potential application in nanotechnology. We have recently found that the T:T mismatched base pair binds with Hg(II) ions to generate a novel metal-mediated base pair in duplex DNA. The thermal stability of the duplex with the T-Hg-T base pair was comparable to that of the corresponding T:A or A:T. The novel T-Hg-T base pair involving the natural base thymine is more convenient than the metal-mediated base pairs involving artificial bases due to the lack of time-consuming synthesis. Here, we examine the specificity and thermodynamic properties of the binding between Hg(II) ions and the T:T mismatched base pair. Only the melting temperature of the duplex with T:T and not of the perfectly matched or other mismatched base pairs was found to specifically increase in the presence of Hg(II) ions. Hg(II) specifically bound with the T:T mismatched base pair at a molar ratio of 1:1 with a binding constant of 10(6) M(-1), which is significantly higher than that for nonspecific metal ion-DNA interactions. Furthermore, the higher-order structure of the duplex was not significantly distorted by the Hg(II) ion binding. Our results support the idea that the T-Hg-T base pair could eventually lead to progress in potential applications of metal-mediated base pairs in nanotechnology.     

Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.     

Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis

Non-canonical base pairs contribute immensely to the structural and functional variability of RNA, which calls for a detailed characterization of their spatial conformation. Intra-base pair parameters, namely propeller, buckle, open-angle, stagger, shear and stretch describe structure of base pairs indicating planarity and proximity of association between the two bases. In order to study the conformational specificities of non-canonical base pairs occurring in RNA crystal structures, we have upgraded NUPARM software to calculate these intra-base pair parameters using a new base pairing edge specific axis system. Analysis of base pairs and base triples with the new edge specific axis system indicate the presence of specific structural signatures for different classes of non-canonical pairs and triples. Differentiating features could be identified for pairs in cis or trans orientation, as well as those involving sugar edges or C-H-mediated hydrogen bonds. It was seen that propeller for all types of base pairs in cis orientation are generally negative, while those for trans base pairs do not have any preference. Formation of a base triple is seen to reduce propeller of the associated base pair along with reduction of overall flexibility of the pairs. We noticed that base pairs involving sugar edge are generally more non-planar, with large propeller or buckle values, presumably to avoid steric clash between the bulky sugar moieties. These specific conformational signatures often provide an insight into their role in the structural and functional context of RNA.     

碱基对在DNA双螺旋链上分离的自由能计算

DNA是大部分生物包括病毒的基因载体。DNA双螺旋链通过A＝T和G≡C两种碱基对编码实现对遗传信息的存储。碱基对中的相互作用对DNA双螺旋链的稳定性起到重要作用,直接关系到基因的复制和转录。当前研究中,我们构建了四组不同结构的DNA双螺旋链,进行了总共4.3 μs的分子动力学模拟。通过伞形取样技术计算了DNA双螺旋链中碱基对分离的自由能曲线,并从分子尺度细节和相互作用能对自由能曲线进行解析。在碱基对G≡C的自由能曲线(PMF-PGC)上观察到三个峰,通过监测氢键数目的变化发现分别对应于G≡C三个氢键的断裂;而在A＝T的自由能曲线(PMF-PAT)上只出现一个峰,说明A＝T的两个氢键在分离过程中几乎同时断裂。PMF-PGC的总能垒比PMF-PAT高,主要是因为G≡C比A＝T多一个氢键,更稳定。两条曲线的后段自由能仍然升高,而此时碱基对的氢键已断裂,这是DNA链骨架刚性所导致。我们还研究了碱基对稳定性受相邻碱基对的影响,发现邻近G≡C碱基对会增强A＝T的稳定性, C≡G会削弱A＝T的稳定性, T＝A对A＝T的影响较小。     

Ion trap collisional activation of the deprotonated deoxymononucleoside and deoxydinucleoside monophosphates

Deoxymononucleoside and deoxydinucleoside monophosphate anions formed by electrospray have been subjected to ion trap collisional activation. The threshold for decomposition via loss of base is significantly lower for the deoxymononucleoside 3′-monophosphates than for the corresponding 5′-monophosphates, which indicates that the presence of a charged 3′ phosphate group facilitates base loss. The behavior of the bases among each class of isomers shows slight variation in threshold and tandem mass spectrometry efficiency with tile notable exception of 2′-deoxyguanosine 5′-monophosphate. This ion is exceptionally stable toward decomposition via base loss, which reflects a strong hydrogen bonding interaction between the base and the phosphate group. All dinucleotides fragment via similar mechanisms, but the propensity for neutral base loss relative to loss of a charged base is highly dependent on the identities of both the 5′ and 3′ bases. The behavior of the dinucleotides under collisional activation conditions supports the proposal that base loss proceeds via a proton-bound dimer intermediate in which loss of the charged base directly competes with loss of the neutral base. Application of the kinetic method allows for quantitative predictions of the differences of the gas-phase acidities of the dimer components.     

Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G** level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.     

Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs

For certain DNA hairpin loops, a CG closing base pair has enhanced stability over other closing base pairs, which cannot be explained by the current nearest-neighbor model. We report the use of three-carbon (C3) spacers to investigate the expandability of DNA hairpin loops and the coupling between the loop and closing base pair. Inserting the C3-spacers at most positions in these model loops produced only a modest stabilization or destabilization except for insertion between the 5' end of the loop and the CG closing base pair, which gave a large destabilization. Further investigation on tetraloops and triloops with other closing base pairs established that this destabilization is specific to the unusually stable CG closing base pair. Studies with the nucleotide analogues 2-aminopurine and 2,6-diaminopurine indicated that this stabilization may be due to coupling between functional groups on the first base of the loop and the CG closing base pair. The C3-spacers provide a simple way to interrupt potential interactions and thereby probe loop/stem coupling.     

Effect of loop distortion on the stability and structural dynamics of DNA hairpin and dumbbell conjugates

The thermal stability and conformational dynamics of DNA hairpin and dumbbell conjugates having short A-tract base pair domains connected by tri- or hexa(ethylene glycol) linkers is reported. The formation of stable base-paired A-tract hairpins having oligo(ethylene glycol) linkers requires a minimum of four or five A-T base pairs. The formation of base-paired dumbbells having oligo(ethylene glycol) linkers by means of chemical ligation of nicked dumbbells requires a minimum of two A-T base pairs on either side of the nick. Molecular modeling indicates that the hexa(ethylene glycol) linker is sufficiently long to permit formation of strain-free loop regions and B-DNA base pair domains. In contrast, the tri(ethylene glycol) is too short to permit Watson-Crick base pairing between the bases attached to the linker. The shorter linker distorts the duplex, resulting in fluxional behavior in which the base pairs adjacent to the linker and at the open end of the hairpin dissociate on the nanosecond time scale. The loss of interstrand binding energy caused by these fluctuations leads to a difference of approximately 5 degrees C in melting temperature between EG3 and EG6 hairpins. An analysis of the fluxional behavior of the EG3 adjacent base-pair has been used to study the pathways for base flipping and base stacking, including the identification of rotated base (partially flipped) intermediates that have not been described previously for A-T base pairs.     

The Protonated Guanine–Cytosine Base Pair

Protonated base pairs were recently implicated in the context of DNA proton transfer and charge migration. The effects of protonating different sites of the guanine–cytosine (GC) base pair are studied here by using the DZP++ B3LYP density functional method. Optimized structures for the protonated GC base pair are compared with those of parent GC and the neutral hydrogenated GC radical (GCH). Proton and hydrogen‐atom additions significantly disturb the structure of the GC base pair. However, the structural perturbations arising from protonation are often less than those arising from hydrogenation of GC. Protonation of the GC base pair causes significant strengthening of the interstrand hydrogen bonds and a concomitant increase in the base dissociation energies. The adiabatic ionization potentials (AIPs), vertical ionization potentials (VIPs), and proton affinities (PAs) for the different protonation sites of the GC base pair are predicted. The N7 site of guanine is the preferred site for protonation of the GC base pair.     

催化裂化汽油固体碱预碱洗的研究──负载固体碱对硫化氢的吸附过程分析

以活性炭为载体,碱金属化合物为活性组分,制备出负载固体碱,对其吸附硫化氢性能进行了研究。结果表明,此类固体碱吸附硫化氢能力较强,在固体碱孔外主要进行化学吸附,在固体碱孔内以物理吸附为主,化学吸附和物理吸附能力分别与固体碱、固体碱孔内所负载活性组分的量有关     

铂配合物与DNA碱基对间相互作用的理论研究

用量子化学方法研究一系列Pt(II)配合物作用于嘌呤碱基N7位点后对Watson-Crick碱基对AT、GC的影响. 计算结果显示铂配体与碱基对AT、GC的作用以静电作用为主，同时极化作用也是影响GC碱基对的重要因素. 静电作用极大地增强了铂化嘌呤碱基与嘧啶碱基间的相互作用，而嘌呤碱基与嘧啶碱基间作用与未铂化碱基对作用相近. Pd(II) 和 Ni(II)的相关研究得到类似的结果. 碱基对间氢键作用“二阶微扰能”分析结果与氢键强弱变化一致.     

Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix

Base flipping is a structural mechanism common to many DNA processing and repair enzymes. Changes in the local backbone torsions that occur during base flipping and the effect of environment on their behavior are of particular interest in understanding different base flipping mechanisms. In the present study, structures sampled during umbrella sampling molecular dynamics (MD) simulations of base flipping in aqueous and protein-bound environments, carried out with two different MD simulation strategies, are analyzed to find the most significant phosphodiester backbone distortions in the vicinity of the flipping base. Torsional sampling on the 5' side of the flipping base during flipping through the major groove shows similarities to the torsional sampling on the 3' side during flipping through the minor groove and vice versa. In differing environments, this behavior varies only marginally. These compensating torsional changes in the DNA backbone on 5' and 3' sides of the flipping base limit overall distortion of the DNA double helix during single base flipping. Rotameric intermediate states observed during base flipping are identified and postulated to be metastable states implicated in both large-scale structural changes and functional effects of chemical modifications in DNA.