Repair processes on deoxyribonucleic acid

Many cells have the ability to recognize and eliminate damage to their DNA, particularly thymine dimers formed by UV light. The elimination of this damage may be achieved by enzymatic, light-dependent cleavage of the dimers into the monomers (photoreactivation) or more frequently by dark repair, in which the damaged part is completely removed from the, DNA. In this repair process, the DNA is incised by an endonuclease in the immediate vicinity of the thymine dimers. Oligonucleotides containing the thymine dimer are removed hydrolytically from the DNA by the 5→3′ exonuclease activity of DNA polymerase I (Kornberg enzyme). The resulting gaps are immediately closed by a de novo synthesis with the aid of the same DNA polymerase I, the complementary strand serving as a template (excision repair). The final step is the formation of the phosphodiester bond between the newly synthesized DNA fragment and the old DNA strand by a DNA ligase. Xeroderma pigmentosum patients lack the endonuclease as a result of a genetic defect; they therefore cannot eliminate thymine dimers from their DNA, and are extremely sensitive to sunlight. All information so far suggests that genetic recombination and DNA repair are performed by the same enzyme system.     

Dissecting the differences between the alpha and beta anomers of the oxidative DNA lesion FaPydG

The oxidative DNA lesion, FaPydG rapidly anomerizes to form a mixture of the alpha and beta anomer. To investigate the mutagenic potential of both forms, we prepared stabilized bioisosteric analogues of both configurational isomers and incorporated them into oligonucleotides. These were subsequently used for thermodynamic melting-point studies and for primer-extension experiments. While the beta compound, in agreement with earlier data, prefers cytidine as the pairing partner, the alpha compound is not able form a stable base pair with any natural base. In primer-extension studies with the high-fidelity polymerase Bst Pol I, the polymerase was able to read through the lesion. The beta compound showed no strong mutagenic potential. The alpha compound, in contrast, strongly destabilized DNA duplexes and also blocked all of the tested DNA polymerases, including two low-fidelity polymerases of the Y-family.     

Selective Stabilization of Abasic Site‐Containing DNA by Insertion of Sterically Demanding Biaryl Ligands

Biaryl derivatives that consist of one DNA‐intercalating unit and a sterically demanding component exhibit a specific behavior towards abasic site‐containing DNA (AP‐DNA) as determined by thermal DNA denaturation experiments, spectrometric titrations and CD spectroscopic analysis. Specifically, these ligands strongly stabilize AP‐DNA towards dissociation, whereas they do not or only marginally affect the melting temperature of regular duplex DNA.     

Synthesis and pairing properties of alpha-tricyclo-DNA

We describe the synthesis of the phosphoramidite building blocks of alpha-tricyclo-DNA (alpha-tc-DNA) covering all four natural bases, starting from the already known corresponding alpha-tc-nucleosides. These building blocks were used for the preparation of three alpha-tc-oligonucleotide 10-mers representing a homopurine, a homopyrimidine, and a mixed purine/pyrimidine base sequence. The base-pairing properties with complementary parallel and antiparallel oriented DNA and RNA were studied by UV-melting analysis and CD spectroscopy. We found that alpha-tc-DNA binds preferentially to parallel nucleic acid complements through Watson-Crick duplex formation, with a preference for RNA over DNA. In comparison with natural DNA, alpha-tc-DNA shows equal to enhanced affinity to RNA and also pairs to antiparallel DNA or RNA complements, although with much lower affinity. In the mixed-base sequence these antiparallel duplexes are of the reversed Watson-Crick type, while in the homopurine/homopyrimidine sequences Hoogsteen and/or reversed Hoogsteen pairing is observed. Antiparallel duplex formation of two alpha-tc-oligonucleotides was also observed, although the thermal stability of this duplex was surprisingly low. The base-pairing properties of alpha-tc-DNA are discussed in the context of alpha-DNA, alpha-RNA, and alpha-LNA.     

DNA Nanotechnology-based Biocomputing

With silicon-based microelectronic technology pushed to its limit,scientists hunt to exploit biomolecules to power the bio-computer as substitutes.As a typical biomolecule,DNA now has been employed as a tool to create computing systems because of its superior parallel computing ability and outstanding data storage capability.However,the key challenges in this area lie in the human intervention during the computation process and the lack of platforms for central processor.DNA nanotechnology has created hundreds of complex and hierarchical DNA nanostructures with highly controllable motions by exploiting the unparalleled self-recognition properties of DNA molecule.These DNA nanostructures can provide platforms for central processor and reduce the human intervention during the computation process,which can offer unprecedented opportunities for biocomputing.In this review,recent advances in DNA nanotechnology are briefly summarized and the newly emerging concept of biocomputing with DNA nanostructures is introduced.     

Interlocked DNA Nanojoints for Reversible Thermal Sensing

The ability to precisely measure and monitor temperature at high resolution at the nanoscale is an important task for better understanding the thermodynamic properties of functional entities at the nanoscale in complex systems, or at the level of a single cell. However, the development of high‐resolution and robust thermal nanosensors is challenging. The design, assembly, and characterization of a group of thermal‐responsive deoxyribonucleic acid (DNA) joints, consisting of two interlocked double‐stranded DNA (dsDNA) rings, is described. The DNA nanojoints reversibly switch between the static and mobile state at different temperatures without a special annealing process. The temperature response range of the DNA nanojoint can be easily tuned by changing the length or the sequence of the hybridized region in its structure, and because of its interlocked structure the temperature response range of the DNA nanojoint is largely unaffected by its own concentration; this contrasts with systems that consist of separated components.     

Development of a multiplex system to assess DNA persistence in taphonomic studies

In this study, we have developed a PCR multiplex that can be used to assess DNA degradation and at the same time monitor for inhibition: primers have been designed to amplify human, pig, and rabbit DNA, allowing pig and rabbit to be used as experimental models for taphonomic research, but also enabling studies on human DNA persistence in forensic evidence. Internal amplified controls have been added to monitor for inhibition, allowing the effects of degradation and inhibition to be differentiated. Sequence data for single‐copy nuclear recombination activation gene (RAG‐1) from human, pig, and rabbit were aligned to identify conserved regions and primers were designed that targeted amplicons of 70, 194, 305, and 384 bp. Robust amplification in all three species was possible using as little as 0.3 ng of template DNA. These have been combined with primers that will amplify a bacterial DNA template within the PCR. The multiplex has been evaluated in a series of experiments to gain more knowledge of DNA persistence in soft tissues, which can be important when assessing what material to collect following events such as mass disasters or conflict, when muscle or bone material can be used to aid with the identification of human remains. The experiments used pigs as a model species. When whole pig bodies were exposed to the environment in Northwest England, DNA in muscle tissue persisted for over 24 days in the summer and over 77 days in the winter, with full profiles generated from these samples. In addition to time, accumulated degree days (ADD) were also used as a measure that combines both time and temperature—24 days was in summer equivalent to 295 ADD whereas 77 days in winter was equivalent to 494 ADD.     

Energetics,Conformation, and Recognition of DNA Duplexes Modified by Methylated Analogues of [PtCl(dien)]+

Monodentate DNA binding of [PtCl(dien)]⁺ (dien=diethylenetriamine) complexes may considerably affect the biophysical properties of DNA and consequently downstream cellular processes as a result of a large increase in the bulkiness of the nonleaving ligand by multiple methylation (see illustration).

     

Nick sealing by T4 DNA ligase on a modified DNA template: tethering a functional molecule on D-threoninol

Efficient DNA nick sealing catalyzed by T4 DNA ligase was carried out on a modified DNA template in which an intercalator such as azobenzene had been introduced. The intercalator was attached to a D-threoninol linker inserted into the DNA backbone. Although the structure of the template at the point of ligation was completely different from that of native DNA, two ODNs could be connected with yields higher than 90% in most cases. A systematic study of sequence dependence demonstrated that the ligation efficiency varied greatly with the base pairs adjacent to the azobenzene moiety. Interestingly, when the introduced azobenzene was photoisomerized to the cis form on subjection to UV light (320-380 nm), the rates of ligation were greatly accelerated for all sequences investigated. These unexpected ligations might provide a new approach for the introduction of functional molecules into long DNA strands in cases in which direct PCR cannot be used because of blockage of DNA synthesis by the introduced functional molecule. The biological significance of this unexpected enzymatic action is also discussed on the basis of kinetic analysis.     

Extrachromosomal DNA in bacteria

In addition to chromosomal DNA carrying the genetic information of the cell, many bacterial cells contain smaller circular DNA factors known as plasmids or episomes. These genetic elements endow the cell with additional biochemical capabilities. The fertility factors (F and F′), the antibiotic resistance factors (R), the colicinogenic factors (Col), the hemolytic factors (Hly), and other extrachromosomal DNA systems are described. These small DNA molecules can be isolated, and are therefore particularly suitable for the investigation of DNA replication and the stable establishment of genetic material in the bacterial cell.     

Ladungstransfer durch die DNA: Vom Mechanismus zur Anwendung

DNA charge transfer chemistry has been subject of considerable interest with consequences in the formation of oxidative damage to the DNA which can result in mutagenesis or carcinogenesis. In this article, important examples of spectroscopical and biochemical assays are compared and discussed in terms of the effiencies, rates, and mechanisms. Coupled with the demonstration that such charge transfer can be modulated both negatively and positively by DNA‐binding proteins, these observations therefore suggest the intriguing possibility that DNA‐mediated charge transfer chemistry is biological relevant and may play a role in cellular processes. Additionally, charge transfer chemistry plays a growing role in the recent development of DNA chips detecting mutations or lesions of nucleic acids.     

Near-Quantitative Preparation of Short Single-Stranded DNA Circles

Small, single-stranded DNA (ssDNA) circles have many applications, such as templating rolling circle amplification (RCA), capturing microRNAs, and scaffolding DNA nanostructures. However, it is challenging to prepare such ssDNA circles, particularly when the DNA size becomes very small (e.g. a 20 nucleotide (nt) long ssDNA circle). Often, such short ssDNA dominantly form concatemers (either linear or circular) due to intermolecular ligation, instead of forming monomeric ssDNA circles by intramolecular ligation. Herein, a simple method to overcome this problem by designing the complementary linker molecules is reported. It is demonstrated that ssDNA, as short as 16 nts, can be enzymatically ligated (by the commonly used T4 DNA ligase) into monomeric ssDNA circles at high concentration (100 μM) with high yield (97 %). This method does not require any special sequence, thus, it is expected to be generally applicable. The experimental protocol is identical to regular DNA ligation, thus, is expected to be user friendly for general chemists and biologists.     

Extrahelical damaged base recognition by DNA glycosylase enzymes

The efficient enzymatic detection of damaged bases concealed in the DNA double helix is an essential step during DNA repair in all cells. Emergent structural and mechanistic approaches have provided glimpses into this enigmatic molecular recognition event in several systems. A ubiquitous feature of these essential reactions is the binding of the damaged base in an extrahelical binding mode. The reaction pathway by which this remarkable extrahelical state is achieved is of great interest and even more debate.     

A Reconfigurable DNA Accordion Rack

DNA nanostructure‐based mechanical systems that control the distance between elements of interest have demonstrated great potential for various applications, including nanoplasmonic systems, molecular reactors, and other nanotechnology platforms. However, previously reported systems could not collectively manipulate a 2D or 3D nanoscale network of elements to various forms in multiple stages. A reconfigurable DNA accordion rack structure is introduced that is a DNA beam lattice that changes its conformation with a small amount of short‐length DNA locks as the controlling input. The lattice shape of the 2D DNA accordion rack and the diameter and the height of the 3D DNA nanotubular structure made of the DNA accordion rack could be controlled. Furthermore, by sequentially repeating the detachment and the attachment of the different DNA locks using strand displacement, the shape reconfiguration was repeatedly carried out.     

Programmable Assembly of Nano‐architectures through Designing Anisotropic DNA Origami Patches

Programmable assembly of nanoparticles (NPs) into well‐defined architectures has attracted attention because of tailored properties resulting from coupling effects. However, general and precise approaches to control binding modes between NPs remain a challenge owing to the difficulty in manipulating the accurate positions of the functional patches on the surface of NPs. Here, a strategy is developed to encage spherical NPs into pre‐designed octahedral DNA origami frames (DOFs) through DNA base‐pairings. The DOFs logically define the arrangements of functional patches in three dimensions, owing to the programmability of DNA hybridization, and thus control the binding modes of the caged nanoparticle with designed anisotropy. Applying the node‐and‐spacer approach that was widely used in crystal engineering to design coordination polymers, patchy NPs could be rationally designed with lower symmetry encoded to assemble a series of nano‐architectures with high‐order geometries.     

多羟乙基双核大环多胺La（Ⅲ）配合物对双对硝基苯酚磷酸二酯和DNA催化水解作用研究

合成了一类新型多羟乙基双核大环多胺La(Ⅲ)配合物,其结构经1H NMR,MS,元素分析等表征.通过紫外分光光谱法和琼脂糖凝胶电泳技术,研究了双核大环多胺La(Ⅲ)配合物催化双对硝基苯酚磷酸二酯的水解反应和对质粒DNA(pUC18)的催化水解作用.结果表明:双核大环多胺La(Ⅲ)配合物可以有效催化双对硝基苯酚磷酸二酯水解和促进质粒DNA在生理条件下的水解裂解.双对硝基苯酚磷酸二酯的水解速率提高了2.36×104倍.讨论了配合物结构对水解反应的影响.