Oxidation of DNA Bases Influenced by the Presence of Other Bases

Electrochemical detection of DNA is a highly important topic. Here we show that the electrochemical responses of one DNA base (guanine, adenine, cytosine or thymine), in terms of oxidation potential, current intensity, peak width and resolution can be highly influenced by the presence of other DNA bases at electrochemically reduced graphene oxide (ER‐GO) as well as standard glassy carbon electrode. We have observed that the effects were more significant for adenine base on ER‐GO and cytosine base on glassy carbon (GC) electrode. Differences in responses were generally low in a mixture of four different DNA bases but interestingly, deviations become significantly larger when only one or two other bases were present. Our findings are of paramount importance for future developments in DNA detection and analysis since individual DNA bases are not present in isolation in nature or in typical biosensing systems.     

DNA Hydrolysis and Voltammetric Determination of Guanine and Adenine Using Different Electrodes

Abstract

This work reports the development of a biosensor method for the label‐free detection of specific DNA sequences. In the initial phase, square wave voltammetry (SWV) was used in a comparative investigation into the electrochemical oxidation of purines (guanine and adenine) and DNA fragments at various electrode surfaces: carbon paste (CPE), glassy carbon electrode (GCE), and gold (AuE). Relative to the carbon electrodes, an approximate 4.0‐fold, 6.0‐fold, and 3.25‐fold increase in the anodic response was observed when guanine, adenine, and hydrolyzed DNA, respectively, were measured on the AuE. It was shown that the guanine and adenine bases could be successfully determined by use of SWV for a deoxyribonucleic acid sample following acid hydrolysis. This label‐free detection of hydrolyzed DNA on gold electrodes has significant advantages over methods using existing carbon electrode materials because of its higher sensitivity and the potential applicability of microfabrication techniques for the production of the requisite gold electrodes.

In another phase of development, the times and conditions for DNA hydrolysis and purine release were investigated. It was shown that under optimal conditions, trace levels of the purine bases could be readily detected following 20 min of hydrolysis at room temperature. The proposed method can be used to estimate the guanine and adenine contents in DNA with in a linear range of 5–30 ng ml^?1.

Finally, when appropriate probe sequences were first adsorbed on the surface of the screen‐printed gold electrode (SPGE), this electrochemical biosensor could be used to specifically detect sequences from ss corona virus aviair following hybridization and hydrolysis reactions on the sensor surface. No enhancement of the voltammetric response was observed when the sensor was challenged with a non‐complementary DNA sequence.     

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.     

Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold

A comparison of the binding of DNA bases (adenine, cytosine, guanine, and thymine) and nucleosides (2'deoxyadenosine, 2'deoxycytidine, 2'deoxyguanosine, and thymidine) to gold thin films is presented. Desorption of monolayer/submonolayer and multilayer films of the adsorbates on gold studied via temperature-programmed desorption (TPD) and reflection-absorption infrared (RAIR) spectroscopy reveals that there are major differences in the binding affinities of the different bases to gold, for example, thymine DeltaHdes = 111 +/- 2 kJ/mol compared to guanine DeltaHdes = 146 +/- 2 kJ/mol. The differences can be rationalized by molecular structures of the bases and their binding modes to gold surfaces deduced from IR data. Similar trends in desorption energies, shifted to lower desorption energy by more than 10 kJ/mol, are observed for deoxynucleoside layers on gold thin films.     

DNA碱基与高氯酸根共吸附行为的表面增强拉曼光谱研究

共吸附有助于实现弱吸附分子或离子的高灵敏表面增强拉曼光谱(SERS)检测.本文研究了四种脱氧核糖核酸(DNA)碱基,即腺嘌呤、鸟嘌呤、胞嘧啶、胸腺嘧啶与高氯酸根(ClO4-)在金纳米粒子表面的共吸附行为,并考察了吸附能力、电位、共存阴离子等因素的影响.研究发现四种碱基在质子化后都可以与ClO4-发生共吸附,但在金表面吸附能力弱的胸腺嘧啶与ClO4-共吸附所获得的ClO4-信号最弱.另外,负电位下电极的排斥作用,以及较正电位下基底SERS增强效应减小等因素都会导致ClO4-信号衰减.此外,Cl-、NO3-、SO24-等阴离子可以与ClO4-发生可逆动态竞争共吸附,同时引起ClO4-信号减弱.以上结果将为提高共吸附法检测弱吸附离子的灵敏度提供重要参考.     

Gas phase interaction of zinc ion with purine and pyrimidine DNA and RNA bases

The interaction of uracil, thymine, cytosine, adenine, and guanine with zinc ion was studied at the density functional B3LYP/6‐311+G(2df,2p) level. Different binding sites allowing both mono‐metal and bi‐metal coordination were considered for the different low‐lying tautomers of nucleic acid bases. Zinc ion forms stable compounds with all nucleobases. Except for cytosine, mono‐coordination appears to be less favored than bi‐coordination in the other pyrimidines. Instead, the preferred sites in the case of adenine and guanine were found to be the N7 and O6 and N7 and N6 pairs of atoms, respectively. Zinc ion affinity was evaluated for all the complexes and compared with values previously obtained for other transition metal ions. In the present case, the following order of metal ion affinity (MIA) was found: G>A>C>T>U. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Bond energies and attachments sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase

Gas-phase metal affinities of DNA and RNA bases for the Na(+) and K(+) ions were determined at density functional level employing the hybrid B3LYP exchange correlation potential in connection with the 6-311+G(2df,2p) basis set. All the molecular complexes, obtained by the interaction between several low-lying tautomers of nucleic acid bases and the alkali ions on the different binding sites, were considered. Structural features of the sodium and potassium complexes were found to be similar except in some uracil and thymine compounds in which the tendency of potassium ion toward monocoordination appeared evident. B3LYP bond energies for both metal ions were in agreement with the available experimental results in the cases of uracil and thymine for which the most stable complex was obtained starting from the most stable tautomer of the free nucleic acid base. For adenine, although the interaction of the ions with the most stable free tautomer generated the least stable molecular complex, the best agreement with experiment was found in just this case. For the remaining cytosine and guanine bases, our calculations indicated that the metal ion affinity value closest to experiment should be determined taking into account the role played by the different tautomers of the free bases with similar energy and all the possible complexes obtained by them.     

Interaction of angelicin with DNA‐bases (III) DFT and ab initio second‐order Moeller–Plesset study

Angelicin geometry was optimized at MP2/6‐31+G(d,p) level and compared with X‐ray experimental data. The highest π‐electron density was found to be localized on C1? C2 and on C13? C14 as confirmed by the calculated bond length and bond order values. Spectrophptometric properties of angelicin were measured and compared with the computed within the TD‐DFT. Quantum chemical methods were used to study the interaction of angelicin, as a nonlinear furocoumarin, with DNA bases and base pairs. The interactions with DNA bases and base pairs were studied to shade more light on the nature of the intercalation binding forces between angelicin and DNA. Comparing computed electronic properties of angelicin with that of linear psoralens show that the former is a weaker intercalator. The geometry of complexes of angelicin with adenine, thymine, adenine–thymine base pair, cytocine, guanine as well as cytocine–guanine base pair have been optimized in two main orientations, planar and stacked, at the levels of B3LYP/cc‐pVDZ, MP2/6‐31G(d,p) and MP2/cc‐pVDZ. Effect of vertical distance and rotational angle between the stacked molecules on the interaction energy were investigated by the aforementioned methods in gas phase and water media. It was found that ab initio methods which account for the electron correlation effects are the minimum level for studying the noncovalent interactions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Transport Selectivity of a Diethylene Glycol Dimethacrylate- Based Thymine-imprinted Polymeric Membrane over a Cellulose Support for Nucleic Acid Bases

The binding mechanism between 9-vinyladenine and pyrimidine base thymine in methanol was studied with UV-visible spectrophotometric method. Based on this study, using thymine as a template molecule, 9-vinyladenine as a novel functional monomer and diethylene glycol dimethacrylate as a new cross-linker, a specific diethylene glycol dimethacrylate-based molecularly imprinted polymeric membrane was prepared over a cellulose support. Then, the resultantly polymeric membrane morphologies were visualized with scanning electron microscopy and its permselectivity was examined using thymine, uracil, cytosine, adenine and guanine as substrates. This result showed that the imprinting polymeric membrane prepared with diethylene glycol dimethacrylate exhibited higher transport capacity for the template molecule thymine and its optimal analog uracil than other nucleic acid bases. The membrane also took on higher permselectivity than the imprinted membrane made with ethylene glycol dimethacrylate as a cross-linker. When a mixture including five nucleic acid bases thymine, uracil, cytosine, adenine and guanine passed through the diethylene glycol dimethacrylate-based thymine-imprinted polymeric membrane, recognition of the membrane for the template molecule thymine and its optimal analog uracil was demonstrated. It was predicted that the molecularly imprinted membrane prepared with diethylene glycol dimethacrylate as cross-linker might be applicable to thymine assay of absolute hydrolysates of DNA or uracil assay of absolute hydrolysates of RNA in biological samples because of its high selectivity for the template molecule thymine and its optimal analog uracil.     

Theoretical study of the interaction pattern and the binding affinity between procaine and DNA bases

The interacting patterns and mechanism of the binding affinity between the local anaesthetic procaine and four DNA bases (adenine, cytosine, guanine and thymine) in neutral form have been investigated in gas phase using the Austin Model l and density functional methods. The results show that the complexes are mainly stabilized by the H-bonding interactions. The bond critical point properties of the optimized complexes were analyzed by using the atoms in molecules theory with DFT method and the results show that the presence of the C?H···O or C?H···N hydrogen bonding. The natural bond orbital analysis was performed to quantitatively evaluate the hydrogen bonding interaction. The interacting energy shows that the binding of procaine with guanine is the most strong, whereas its binding to cytosine exhibits relatively weaker stability. The strength order of the relevant transferred charge between procaine and DNA base with natural population analysis are consist with the HOMO–LUMO gap results for each complex. And the order is accord with the relevant electrochemical experimental results.     

MP2 study on the hydrogen-bonding interaction between 5-hydroxymethyl-uracil and DNA bases: A,C, G,T

The 5-hydroxymethyl-uracil (HmU) is a product of oxidative attack on the methyl group of thymine in DNA. In this work, we present the hydrogen bonding complexes formation involving HmU bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys-Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: HmU:A > HmU:G > HmU:C > HmU:T.     

Structural basis for bifunctional zinc(II) macrocyclic complex recognition of thymine bulges in DNA

The zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane (cy4q) binds selectively to thymine bulges in DNA and to a uracil bulge in RNA. Binding constants are in the low-micromolar range for thymine bulges in the stems of hairpins, for a thymine bulge in a DNA duplex, and for a uracil bulge in an RNA hairpin. Binding studies of Zn(cy4q) to a series of hairpins containing thymine bulges with different flanking bases showed that the complex had a moderate selectivity for thymine bulges with neighboring purines. The dissociation constants of the most strongly bound Zn(cy4q)-DNA thymine bulge adducts were 100-fold tighter than similar sequences with fully complementary stems or than bulges containing cytosine, guanine, or adenine. In order to probe the role of the pendent group, three additional zinc(II) complexes containing 1,4,7,10-tetraazacyclododecane (cyclen) with aromatic pendent groups were studied for binding to DNA including 1-(2-quinolyl)methyl-1,4,7,10-tetraazacyclododecane (cy2q), 1-(4-biphenyl)methyl-1,4,7,10-tetraazacyclododecane (cybp), and 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-N,N-dimethylnaphthalen-1-amine (dsc). The Zn(cybp) complex binds with moderate affinity but little selectivity to DNA hairpins with thymine bulges and to DNA lacking bulges. Similarly, Zn(dsc) binds weakly both to thymine bulges and hairpins with fully complementary stems. The zinc(II) complex of cy2q has the 2-quinolyl moiety bound to the Zn(II) center, as shown by (1)H NMR spectroscopy and pH-potentiometric titrations. As a consequence, only weak (500 μM) binding is observed to DNA with no appreciable selectivity. An NMR structure of a thymine-bulge-containing hairpin shows that the thymine is extrahelical but rotated toward the major groove. NMR data for Zn(cy4q) bound to DNA containing a thymine bulge is consistent with binding of the zinc(II) complex to the thymine N3(-) and stacking of the quinoline on top of the thymine. The thymine-bulge bound zinc(II) complex is pointed into the major groove, and there are interactions with the guanine positioned 5' to the thymine bulge.     

Construction of 5‐amino‐1,10‐phenanthroline‐Fe(II) Nanostructures on Glassy Carbon Electrode: Simultaneous and Selective Determination of Purine and Pyrimidine DNA Bases

5‐amino‐1,10‐phenanthroline‐Fe(II) complex is immobilized onto GC electrode and used for determination of DNA bases. Modifications are traced by electrochemical methods. All DNA bases are electroactive on the modified electrode. The I_ps increased linearly with increase of DNA bases concentration. A wide response range was observed for each base (～4 orders for guanine (GA) and adenine (A); and ～2.5 orders for thymine (T) and cytosine (C)) with DLs of 0.15, 4.44, 133.0 and 230.0 nM, respectively. The electrode was applied for determination of calf‐thymus DNA bases. The value obtained for [(GA+C)/(A+T)], 0.78, is in good agreement with standard value, 0.77.     

MP2 study on the hydrogen bonding interaction between 5-hydroxy-5-methylhydantoin and DNA bases: A,C, G,T

The 5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this study, we present the hydrogen bonding base pairs involving 5-OH-5-Me-dHyd bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: 5-OH-5-Me-dHyd:G>5-OH-5-Me-dHyd:A>5-OH-5-Me -dHyd:C~5-OH-5-Me-dHyd:T.     

Base pairing patterns of DNA base lesion spiroiminodihydantoin: A DFT study

The DNA base lesion spiroiminodihydantoin (Sp) is produced in biological systems endogenously and can cause mutation and cancer. It is considered to be more mutagenic and deleterious than 8‐oxoguanine and other oxidized guanine products such as guanidinohydantoin (Gh) and imidazolone. In this work, the base pairing patterns of Sp with each of the normal nucleic acid bases of DNA have been investigated thoroughly using the B3LYP, M06‐2X, and wB97X‐D functionals of density functional theory in conjunction with the aug‐cc‐pVDZ basis set. It is found that the magnitudes of interaction energies between the bases and Sp follow the order: Sp‐guanine >> Sp‐cytosine > Sp‐adenine > Sp‐thymine. The strong Sp‐guanine abnormal base pairing may be the main cause of the observed mutagenicity of Sp. © 2013 Wiley Periodicals, Inc.     

A cyclodextrin host-guest recognition approach to a label-free electrochemical DNA hybridization biosensor

A novel label-free electrochemical DNA hybridization biosensor using a β-cyclodextrin/poly(N-acetylaniline)/carbon nanotube composite modified screen printed electrode (CD/PNAANI/CNT/SPE) has been developed. The proposed DNA hybridization biosensor relies on the intrinsic oxidation signals of guanine (G) and adenine (A) from single-stranded DNA entered into the cyclodextrin (CD) cavity. Due to the binding of G and A bases to complementary cytosine and thymine bases in dsDNA, the signals obtained for ssDNA were much higher than that of dsDNA. The synergistic effect of the multi-walled carbon nanotubes provides a significantly enhanced voltammetric signal, and the CD encapsulation effect makes anodic peaks of G and A shift to less positive potentials than that at the bare SPE. The peak heights of G and A signals are dependent on both the number of the respective bases in oligonucleotides and the concentration of the target DNA sequences. Hybridization of complementary strands was monitored through the measurements of oxidation signal of purine bases, which enabled the detection of target sequences from 0.01 to 1.02 nmol μl(-1) with the detection limit of target DNA as low as 5.0 pmol μl(-1) (S/N = 3). Implementation of label-free and homogeneous electrochemical hybridization detection constitutes an important step toward low-cost, simple, highly sensitive and accurate DNA assay. Discrimination between complementary, noncomplementary, and two-base mismatch targets was easily accomplished using the proposed electrode.     

Functional monomers and polymers. XCIV. Photochemical reactions on the synthetic polymers containing thymine bases in the presence of adenine derivatives

Photodimerization reactions of polyacrylate and polymethacrylate derivatives and the dimer model compound containing thymine bases were studied in the presence of adenine derivatives in dimethyl sulfoxide; N,N-dimethylformamide; and dimethyl sulfoxide–ethylene glycol solutions. The photodimerization of thymine bases both in the polymers and in the dimer model compound was found to be quenched by the addition of adenine derivatives. Base-base interaction in the ground state was also studied by ultraviolet (UV) spectroscopy in the three solvents. The quenching of the photodimerizationof thymine bases in the presence of adenine derivatives was discussed in terms of the specific interaction between adenine and thymine bases both in ground and excited states.     

DNA甲基化-非甲基化碱基间堆积作用的理论研究

运用二级Mфller-Plesset(MP2)理论方法和cc-pVDZ基组优化了6-甲基鸟嘌呤(O6-MethylG),4-甲基胸腺嘧啶(O4-MethylT)以及5-甲基胞嘧啶(C5-MethylC)与DNA碱基鸟嘌呤(G),腺嘌呤(A),胞嘧啶(C),胸腺嘧啶(T)之间的堆积构型.在MP2/aug-cc-pVXZ//MP2/cc-pVDZ(X=D,T)水平上,采用完全基组外推方法校正了堆积碱基对间的相互作用能,并用完全均衡校正法(CP)校正了基组重叠误差(BSSE).MP2计算结果表明,DNA碱基甲基化使得嘧啶-嘧啶、嘧啶-嘌呤堆积碱基间的平行旋转角发生明显改变,并使堆积碱基间的相互作用能增大.在MP2/cc-pVDZ计算级别上得到了各堆积碱基对的全电子波函数,并用分子中的原子理论(AIM)分析了堆积碱基对间的弱相互作用.AIM分析结果显示,甲基化增强了堆积碱基间的π-π作用,且甲基氢与相邻碱基间形成H2CH…X(X=O,N,CH3,NH2)等类型的氢键.甲基化损伤使碱基间重叠程度增大、π-π作用增强以及堆积碱基间形成多个氢键,是堆积作用能增加的主要原因.     

On the structure and desorption dynamics of DNA bases adsorbed on gold: a temperature-programmed study

The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption spectroscopy (TPD-IRAS) and temperature-programmed desorption-mass spectroscopy (TPD-MS). It is shown that the pyrimidines, adenine and guanine, adsorb to gold in a complex manner and that both adhesive (adenine) and cohesive (guanine) interactions contribute the apparent binding energies to the substrate surface. Adenine displays at least two adsorption sites, including a high-energy site (210 degrees C, approximately 136 kJ/mol), wherein the molecule coordinates to the gold substrate via the NH2 group in an sp3-like, strongly perturbed, nonplanar configuration. The purines, cytosine and thymine, display a less complicated adsorption/desorption behavior. The desorption energy for cytosine (160 degrees C, approximately 122 kJ/mol) is similar to those obtained for adenine and guanine, but desorption occurs from a single site of dispersed, nonaggregated cytosine. Thymine desorbs also from a single site but at a significantly lower energy (100 degrees C, approximately 104 kJ/mol). Infrared data reveal that the monolayer architectures discussed herein are structurally very different from those observed for the bases in the bulk crystalline state. It is also evident that both pyrimidines and purines adsorb on gold with the plane of the molecule in a nonparallel orientation with respect to the substrate surface. The results of this work are discussed in the context of improving the understanding of the design of capturing oligonucleotides or DNA strands for bioanalytical applications, in particular, for gold nanoparticle-based assays.     

Gas-phase theoretical prediction of the metal affinity of copper(I) ion for DNA and RNA bases

The most stable tautomeric forms of free DNA and RNA bases were considered as substrates for the interaction of Cu(+) ion. Several suitable attachment sites were selected that involved mono- and bi-coordination of the cation. B3LYP/6-311 + G(2df,2p) bond energies showed that copper ion has the major affinity for guanine and cytosine bases. The proposed values of Cu(+) ion affinity are 59.9, 60.0, 80.2, 88.0 and 69.0 kcal mol(-1) for uracil, thymine, cytosine, guanine and adenine, respectively. The preference for the mono- or bi-coordination depends on the particular tautomer for each base.