银离子对DNA碱基对的横向电输运特性的影响

以密度泛函理论为基础,利用非平衡格林函数方法研究DNA的两碱基对分别与Au电极耦合的两电极体系的电输运特性.首先计算电极-碱基对间距对碱基对横向输运性质的影响,发现碱基对的电导对距离的变化非常敏感,呈剧烈的振荡变化.然后在电极距离固定的情况下,计算系统在低偏压下的横向传输特性,并对与银离子结合前后的碱基对的横向传输特性进行比较.结果发现,加入银离子后,G-C碱基对的导电能力下降,A-T碱基对的电导增大.     

DNA分子链电子结构特性研究

在单电子紧束缚近似下，建立了一维无序二元DNA分子链模型，计算了链长为2×10⁴个碱基对的DNA分子链的电子态密度、局域化特性，并探讨了碱基对的不同组分、格点能量无序度对电子局域态的影响.结果表明：由于DNA分子链中格点能量无序及碱基对的不同组分的存在，其电子波函数呈现出局域化的特性，而局域长度作为衡量电子局域化程度的一个尺度，受碱基对的组分及格点能量无序度的影响. 关键词： DNA分子链 电子结构 电子局域态 局域长度     

Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma

Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.(Communicated by Takao SEKIYA, M.J.A.).     

碱基序列对DNA分子电子结构的影响

将DNA分子看成一维二元随机序列，利用负本征值理论计算其态密度，针对碱基对分布和相对含量等参量，讨论了DNA分子的电子结构.结果表明碱基对分布和相对含量都对电子能态结构影响较大，说明碱基序列对DNA分子的电子结构影响很大. 关键词： DNA分子 电子态密度 碱基对     

Effect of genome sequence on the force-induced unzipping of a DNA molecule

We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force F(y) vs. extension y is found to have a series of maxima and minima. By changing base pairs at selected places in the molecule we calculated the change in F(y) curve and found that the change in the value of force is of the order of few pN and the range of the effect depending on the temperature, can spread over several base pairs. We have also discussed briefly how to calculate in the constant force ensemble a pause or a jump in the extension-time curve from the knowledge of F(y).     

Localized single-stranded bubble mechanism for cyclization of short double helix DNA

Recent experiments indicate that double-stranded DNA molecules of approximately 100 base pairs in length have a probability of cyclization which is up to 10(5) times larger than that expected based on the known bending modulus of the double-helix. We argue that for short molecules, the formation of a few base pairs of single-stranded DNA can provide a "flexible hinge" that facilitates loop formation. A detailed calculation shows that this mechanism explains the experimental data.     

An Insight into the Helicase Functioning Through the Hydrogen Isotope Effects

The replacement of hydrogen atoms by deuterium in hydrogen bonds of base pairs AT and GC decreases the rate of unwinding DNA by more than 30% per each unzipped base pair. In active helicases this isotope effect refers to the ratio of the rate constants for unzipping closed base pairs in protiated and deuterated DNA. In passive helicases the effect is controlled by ratio of equilibrium constants for opening and closing base pairs in protiated and deuterated DNA. Hydrogen/deuterium isotope effects on the unwindening of double strand DNA seems to explain, at least partly, biological and pharmacological effects of heavy water on living organisms and may be used as a means to explore new facets of the helicase functioning.     

Anharmonic Vibrational Signatures of DNA Bases and Watson-Crick Base Pairs

在密度泛函理论水平上研究了从DNA碱基单体到Watson-Crick碱基对的结构、电荷分布、以及非谐性振动参数的变化. 通过研究参与碱基对中多重氢键的NH₂、N-H和C=O的伸缩振动模式,预测了这些模式的对角非谐性常数、非对角非谐性常数、以及非谐性振动耦合对碱基结构变化的敏感性. 研究结果揭示了DNA碱基中非谐性振动势、分子间氢键和静电相互作用之间的内在联系.     

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.     

IR Vibrational spectra of H-bonded complexes of adenine, 2-aminopurine and 2-aminopurine<Superscript>+</Superscript> with cytosine and thymine: Quantum-chemical study

Using theoretical study on the B3LYP/6-311++G(d,p) level of theory, we have compared vibrational spectra of 2-aminopurine (as neutral or protonated at N1 atom species) with adenine and H-bonded complexes of 2-aminopurine (as neutral or protoned at N1 atom species) · cytosine or 2-aminopurine · thymine with adenine · cytosine and adenine · thymine base pairs. The nature of the base pairing between adenine, 2-aminopurine, 2-aminopurine⁺ and cytosine or thymine have been investigated by means of quantum-mechanical calculations. We have investigated the effect of the hydrogen bond formation on the vibrational spectra of the investigated base pairs. The main differences in the vibrational spectra as for bases so for base pairs have been observed in the high-frequency region.     

Raman spectroscopic studies on the conformational changes of calf thymus DNA induced by Cd2+ ions

We used Raman spectroscopy to study the conformational changes of DNA induced by Cd2+ ions in different Cd2+ concentrations solution. The experimental results show that when the Cd2+/PO-2 ratio R increased from 0 to 3.0, the band 835.0 cm-1 shifted about 8 cm-1, and the overlapping spectra of 1446.0and 1461.0 cm-1 separated and moved to 1441.0 and 1458.0 cm-1, respectively. This indicates that the conformation of DNA has changed from a "normal" B-form to a "modified" B'-form. At the same time,changes of other bands demonstrate that parts of base stacking collapse and some hydrogen bonds between AT are disrupted, AT base pairs are damaged more larger than GC base pairs.     

两种卤代荧光素与DNA作用荧光特性的研究

对四溴荧光素(TBF)、四氯四溴荧光素(TTF)两种卤代荧光素与DNA作用的荧光特性进行了研究,结果表明：TBF和TTF的最大λ_ex/λ_em为518/540 nm和540/560 nm,DNA的存在会使TBF和TTF的荧光强度发生变化;荧光猝灭实验和偏振实验表明：TBF与DNA的作用方式可能是沟槽键合和嵌插作用,而TTF 嵌插在了DNA碱基对之间;盐效应实验表明：溶液离子强度的大小会影响TBF和TTF与DNA的作用;荧光法测得TBF和TTF与DNA的结合常数为1×106和2×106 L·mol-1,结合位点数为0.62和0.16。     

Sequence recognition in the pairing of DNA duplexes

Pairing of DNA fragments with homologous sequences occurs in gene shuffling, DNA repair, and other vital processes. While chemical individuality of base pairs is hidden inside the double helix, x ray and NMR revealed sequence-dependent modulation of the structure of DNA backbone. Here we show that the resulting modulation of the DNA surface charge pattern enables duplexes longer than approximately 50 base pairs to recognize sequence homology electrostatically at a distance of up to several water layers. This may explain the local recognition observed in pairing of homologous chromosomes and the observed length dependence of homologous recombination.     

阿克拉霉素A与DNA作用的光谱学研究

文章研究了阿克拉霉素A(ACR)吸收光谱和荧光光谱特性及其与DNA的相互作用。研究结果表明, ACR荧光光谱和吸收光谱受pH值影响较大,且随DNA加入产生减色效应。通过计算, ACR与DNA的结合常数比单纯以嵌入式与DNA结合的蒽醌类化合物大约1～2个数量级为2.7×106 mol·L-1,结合位点数为0.67碱基对,ACR与DNA结合方式复杂,ACR为非经典嵌入剂。     

乙酸对DNA空间结构微观损伤的Raman光谱特征

利用Raman光谱技术从分子水平研究了乙酸对鲱鱼精DNA空间结构微观损伤的特征。实验结果表明,鲱鱼精DNA被乙酸浸润处理后,Raman特征频率与强度均发生了不同程度的变化。证明了乙酸对DNA的损伤是整个分子,包括骨架磷酸基团、脱氧核糖及碱基。不仅是DNA的构象,而且其构型也发生了变化：氢键断裂,B型构象被修改,DNA单、双链断裂,碱基也受到了严重损伤。其碱基损伤严重程度依次为胞嘧啶、胸腺嘧啶、鸟嘌呤和腺膘呤。     

DNA纤维质子化及脱嘧啶的拉曼光谱研究

对鲱精DNA纤维用pH 1 85酸溶液处理不同时间后 ,将样品进行拉曼光谱分析。结果表明DNA分子发生明显的质子化作用 ,有部分GC碱基对之间形成Hoogsteen型氢键的证明。酸不仅导致了DNA中部分嘌呤的脱落 ,同时还有部分嘧啶的脱落 ,其原因与嘧啶的质子化可能强于嘌呤有关。质子化、脱嘌呤、脱嘧啶的共同作用进一步引起原有正常配对的氢键断裂 ,DNA分子内双链状态不稳定 ,可见酸处理DNA时发生了酸变性这一现象 ,但其产物性质显著不同于热变性或碱变性产物。     

Thermal denaturation of DNA molecules: A comparison of theory with experiment

Experimental and theoretical results on the helix-coil transition of DNA are reviewed. The theoretical model of the transition is described, and the influence of heterogeneous base pair stacking, and strand dissociation on the predicted melting transition is examined. New experimental transition data on seven DNAs, 154–587 base pairs (bp) long, are reported and compared with theoretical calculations. We review and evaluate previous studies on long DNAs (≥1000 bp) as well as previous and recent results on short DNAs. The comparison of theory with equilibrium melting curves of short DNAs indicates that base pair sequence has a relatively small influence on the stacking free energy. Excellent agreement is obtained between theory and equilibrium transitions of 14 out of 15 fragments 80–587 pb. The deviation between theory and experiment for a 516 bp DNA can be attributed to the formation of stem-loop structures. This may provide the explanation for inconsistent results observed with long DNAs. The effect of single base pair changes on DNA transitions is discussed. Current views on fluctuational opening of base pairs at temperatures below the transition are described.     

Envisaging quantum transport phenomenon in a muddled base pair of DNA

The effect of muddled base pair on electron transfer through a deoxyribonucleic acid (DNA) molecule connected to the gold electrodes has been elucidated using tight binding model. The effect of hydrogen and nitrogen bonds on the resistance of the base pair has been minutely observed. Using the semiempirical extended Huckel approach within NEGF regime, we have determined the current and conductance vs. bias voltage for disordered base pairs of DNA made of thymine (T) and adenine (A). The asymmetrical behaviour amid five times depreciation in the current characteristics has been observed for deviated Au–AT base pair–Au devices. An interesting revelation is that the conductance of the intrinsic AT base pair configuration attains dramatically high values with the symmetrical zig-zag pattern of current, which clearly indicates the transformation of the bond length within the strands of base pair when compared with other samples. A thorough investigation of the transmission coefficients T(E) and HOMO–LUMO gap reveals the misalignment of the strands in base pairs of DNA. The observed results present an insight to extend this work to build biosensing devices to predict the abnormality with the DNA.     

Optimization and analysis of multi-layer diffractive optical elements in visible waveband

An optimization for diffraction efficiency of the multi-layer diffractive optical elements (MLDOEs) is presented, then the construction process of optimization program is introduced in detail. A new optimization initial point is proposed, which contributes to analyze the relationship between the optimal relief heights and the base materials. Through the optimization examples, diffraction efficiency higher than 99.7% from F line (486.1327 nm) to C line (656.2725 nm) of visible waveband can be achieved, and the polychromatic integral diffraction efficiency (PIDE) over the entire waveband is 99.94%. Moreover, this paper compares and analyzes optimization results of different glass pairs, and the relationship between the optimal relief heights pairs and base materials pairs is obtained.     

Breather trapping and breather transmission in a DNA model with an interface

We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are oriented in opposite directions. The Hamiltonian of the Peyrard-Bishop model is augmented with a term that includes the dipole-dipole coupling between base pairs. Numerical simulations show the existence of two dynamical regimes. If the translational kinetic energy of a moving breather launched towards the interface is below a critical value, it is trapped in a region around the interface collecting vibrational energy. For an energy larger than the critical value, the breather is transmitted and continues travelling along the double strand with lower velocity. Reflection phenomena never occur. The same study has been carried out when a single dipole is oriented in opposite direction to the other ones. When moving breathers collide with the single inverted dipole, the same effects appear. These results emphasize the importance of this simple type of local inhomogeneity as it creates a mechanism for the trapping of energy. Finally, the simulations show that, under favorable conditions, several launched moving breathers can be trapped successively at the interface region producing an accumulation of vibrational energy. Moreover, an additional colliding moving breather can produce a saturation of energy and a moving breather with all the accumulated energy is transmitted to the chain.