Electrochemical DNA Hybridization Detection Using DNA Cleavage

We report the new method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture probe DNA, thiolated single strand DNA labeled with electroactive ferrocene group, was immobilized on a gold electrode. After hybridization of target DNA of complementary and noncomplementary sequences, nonhybridized single strand DNA was cleaved using S1 nuclease. The difference of enzymatic cleavage on the modified gold electrode was characterized by cyclic voltammetry and differential pulse voltammetry. We successfully applied this method to the sequence‐selective discrimination between perfectly matched and mismatched target DNA including a single‐base mismatched target DNA. Our method does not require either hybridization indicators or other exogenous signaling molecules which most of the electrochemical hybridization detection systems require.     

Triple Helix Formation in a Topologically Controlled DNA Nanosystem

In the present study, we demonstrate single‐molecule imaging of triple helix formation in DNA nanostructures. The binding of the single‐molecule third strand to double‐stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson–Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high‐speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.     

Relative efficiencies of CpM(CO)(n)CH(3) and CpM(CO)(n)Ph (M = Cr,Mo, W,and Fe) complexes in photoinduced DNA cleavage

The relative efficiencies of photoinduced DNA cleavage by complexes of the type CpM(CO)(n)()R (M = Cr, Mo, or W, n = 3, R = CH(3) or Ph; M = Fe, n = 2, R = CH(3) or C(6)H(5)) have been investigated using a plasmid relaxation assay. Only the tungsten and iron complexes reproducibly caused single strand scission, in addition to which the iron systems efficiently gave double strand cleavage. The iron complexes gave strand scission at lower concentrations than the corresponding tungsten systems, with the phenyl complexes producing more damage than the methyl systems.     

Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity

The present work demonstrates a novel signal-off electrochemical method for the determination of DNA methylation and the assay of methyltransferase activity using the electroactive complex [Ru(NH₃)₆]³⁺ (RuHex) as a signal transducer. The assay exploits the electrostatic interactions between RuHex and DNA strands. Thiolated single strand DNA1 was firstly self-assembled on a gold electrode via Au–S bonding, followed by hybridization with single strand DNA2 to form double strand DNA containing specific recognition sequence of DNA adenine methylation MTase and methylation-responsive restriction endonuclease Dpn I. The double strand DNA may adsorb lots of electrochemical species ([Ru(NH₃)₆]³⁺) via the electrostatic interaction, thus resulting in a high electrochemical signal. In the presence of DNA adenine methylation methyltransferase and S-adenosyl-l-methionine, the formed double strand DNA was methylated by DNA adenine methylation methyltransferase, then the double strand DNA can be cleaved by methylation-responsive restriction endonuclease Dpn I, leading to the dissociation of a large amount of signaling probes from the electrode. As a result, the adsorption amount of RuHex reduced, resulting in a decrease in electrochemical signal. Thus, a sensitive electrochemical method for detection of DNA methylation is proposed. The proposed method yielded a linear response to concentration of Dam MTase ranging from 0.25 to 10 U mL⁻¹ with a detection limit of 0.18 U mL⁻¹ (S/N = 3), which might promise this method as a good candidate for monitoring DNA methylation in the future.     

Fluorometric analysis of DNA unwinding (FADU) as a method for detecting repair-induced DNA strand breaks in UV-irradiated mammalian cells

Fluorometric analysis of DNA unwinding (FADU assay) was originally designed to detect X-ray-induced DNA damage in repair-proficient and repair-deficient mammalian cell lines. The method was modified and applied to detect DNA strand breaks in Chinese hamster ovary (CHO) cells exposed to ionizing radiation as well as to UV light. Exposed cells were allowed to repair damaged DNA by incubation for up to 1 h after exposure under standard growth conditions in the presence and in the absence of the DNA synthesis inhibitor aphidicolin. Thereafter, cell lysates were mixed with 0.15 M sodium hydroxide, and DNA unwinding took place at pH 12.1 for 30 min at 20 degrees C. The amount of DNA remaining double-stranded after alkaline reaction was detected by binding to the Hoechst 33258 dye (bisbenzimide) and measuring the fluorescence. After exposure to X-rays DNA strand breaks were observed in all cell lines immediately after exposure with subsequent restitution of high molecular weight DNA during postexposure incubation. In contrast, after UV exposure delayed production of DNA strand break was observed only in cell lines proficient for nucleotide excision repair of DNA photoproducts. Here strand break production was enhanced when the polymerization step was inhibited by adding the repair inhibitor aphidicolin during repair incubation. These results demonstrate that the FADU approach is suitable to distinguish between different DNA lesions (strand breaks versus base alterations) preferentially induced by different environmental radiations (X-rays versus UV) and to distinguish between the different biochemical processes during damage repair (incision versus polymerization and ligation).     

Comb-type cationic copolymer expedites DNA strand exchange while stabilizing DNA duplex

The accelerating effect of cationic substances on the DNA strand exchange reaction between a 20 bp DNA duplex and its complementary single strand was studied. A polycationic comb-type copolymer, that consists of a poly(L-lysine) backbone and a dextran graft chain (PLL-g-Dex) and known to stabilize triplex DNA, expedites the strand exchange reaction under physiological relevant conditions. Electrostatically a small excess of the copolymer let to a 300-1500-fold increase in the DNA strand exchange while large excess of spermine or cetyltrimethylammonium bromide, a cationic detergent known to promote markedly hybridization of complementary DNA strands, shows only a slight effect. The efficacy of the copolymer was not affected by a 10 mM Mg2+ concentration. Notably the copolymer promotes the strand exchange reaction while it stabilizes double-stranded DNA. The stabilization of strand exchange intermediates consisting of the parent duplex and the single strand by the copolymer is believed to be responsible for the observed acceleration behavior.     

THE REPAIR OF DNA STRAND BREAKS IN HUMAN LYMPHOCYTES EXPOSED TO NEAR UV-RADIATION (UVA) AND FAR UV-RADIATION (UVC)

Abstract— UVA irradiation of human lymphocytes induces DNA strand breaks and a portion of these breaks are closed at a slower rate than X-ray induced DNA strand breaks and the strand breaks generated during repair of UVC induced DNA lesions. In addition, the yield of DNA strand breaks in lymphocytes pretreated with UVA radiation and given a subsequent exposure with UVC radiation is higher and shows a slower decrease with increasing repair time in comparison with the expected yield based on additivity between UVA and UVC induced DNA strand breaks. This indicates that UVA delays the closure of the intermediate strand breaks formed in the repair process of UVC induced DNA lesions.     

长链DNA在金基底上的固定化和电化学标记

本文提出在金基底上用阳离子聚电解质———聚二烯丙基二甲基胺氯化物 (poly(dial lyldimethylammoniumchloride) ,PDDA)自组装膜固定长链DNA的方法 ,用DiffuseReflectanceIn frared ,XPS和STM技术进行表征 ,并对DNA杂交进行电化学标记     

SINGLE-STRAND BREAKS INDUCED IN DNA BY VACUUM-ULTRAVIOLET RADIATION

Abstract— The efficiency of vacuum u.v. for producing single-strand breaks in DNA was determined for wavelengths between 58 and 254 nm (corresponding to photon energies of 21·2 and 4·9 eV, respectively) by using the supertwisted RF-DNA of bacteriophage φX174. The cross-section for production of single-strand breaks increases continuously by about 5 orders of magnitude between 5 and 10 eV photon energy, whereas from 11 to 21 eV the number of strand breaks produced per unit of incident radiation energy is approximately constant. Thus, absorption of a 10-eV photon causes DNA strand breaks with maximum efficiency. In addition, the number of electrons liberated from DNA by photons below 10 eV is one or two orders of magnitude higher than the frequency of strand breaks, demonstrating that in this energy range only a small fraction of the ionizations leads to strand breakage in DNA.     

Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design

Toehold‐mediated DNA strand displacement endows DNA nanostructures with dynamic response capability. However, the complexity of sequence design dramatically increases as the size of the DNA network increases. We attribute this problem to the mechanism of toehold‐mediated strand displacement, termed exact strand displacement (ESD), in which one input strand corresponds to one specific substrate. In this work, we propose an alternative to toehold‐mediated DNA strand displacement, termed fuzzy strand displacement (FSD), in which one‐to‐many and many‐to‐one relationships are established between the input strand and the substrate, to reduce the complexity. We have constructed four modules, termed converter, reporter, fuzzy detector, and fuzzy trigger, and demonstrated that a sequence pattern recognition network composed of these modules requires less complex sequence design than an equivalent network based on toehold‐mediated DNA strand displacement.     

Single,double, and multiple double strand breaks induced in DNA by 3-100 eV electrons

Nonthermal secondary electrons with initial kinetic energies below 100 eV are an abundant transient species created in irradiated cells and thermalize within picoseconds through successive multiple energy loss events. Here we show that below 15 eV such low-energy electrons induce single (SSB) and double (DSB) strand breaks in plasmid DNA exclusively via formation and decay of molecular resonances involving DNA components (base, sugar, hydration water, etc.). Furthermore, the strand break quantum yields (per incident electron) due to resonances occur with intensities similar to those that appear between 25 and 100 eV electron energy, where nonresonant mechanisms related to excitation/ionizations/dissociations are shown to dominate the yields, although with some contribution from multiple scattering electron energy loss events. We also present the first measurements of the electron energy dependence of multiple double strand breaks (MDSB) induced in DNA by electrons with energies below 100 eV. Unlike the SSB and DSB yields, which remain relatively constant above 25 eV, the MDSB yields show a strong monotonic increase above 30 eV, however with intensities at least 1 order of magnitude smaller than the combined SSB and DSB yields. The observation of MDSB above 30 eV is attributed to strand break clusters (nano-tracks) involving multiple successive interactions of one single electron at sites that are distant in primary sequence along the DNA double strand, but are in close contact; such regions exist in supercoiled DNA (as well as cellular DNA) where the double helix crosses itself or is in close proximity to another part of the same DNA molecule.     

Formation of pyrazine derivatives from D-glucosamine and their deoxyribonucleic acid (DNA) strand breakage activity

Two pyrazine derivatives [fructosazine (3) and deoxyfructosazine (6)] were simultaneously formed in a solution of D-glucosamine hydrochloride under various conditions. They showed deoxyribonucleic acid (DNA) strand breakage activity in plasmid pBR322 comparable to that of D-glucosamine. The DNA strand breakage by fructosazine (3) was stimulated by Cu2+.     

Binding studies of DNA with Co(III) coordination compound

The binding of Co(bpy)₂dppz³⁺ to calf thymus DNA was investigated by using absorption and emission spectroscopy, DNA melting techniques, cyclic voltammetry, viscosity and electro phoresis measurements, where bpy is 2,2′-bipyridyl, dppz is dipyrido[3,2-a:2′,3′-c] phenazine. The binding compound shm absorption hypochromicity, fluorescence enhancement, and increasing of DNA melting temperature and the specific viscosity. CV measurement shows the shifts in oxidation-reduction potential and change in peak current with addition of DNA. The compound ie also shown to be more efficient photosensitisers for strand breaks in plasmid DNA.     

金属有机配合物对DNA的断链作用

过渡金属配合物催化DNA、RNA的断链反应研究是近年来最为活跃的前沿研究领域之一,因某些金属配合物具有核酸酶特异性催化DNA、RNA断链的功能,因而该研究对新型抗肿瘤、抗艾滋病化学药物的定向设计及其基因治疗和分子生物学研究中DNA、RNA的高度专一性定点断裂、染色体图谱分析及DNA定位诱变、基因工程中足迹技术(footprinting)以及DNA构象识别等方面均具有重要意义和应用前景,文献已报道了一些具有断裂DNA、RNA功能的金属配合物,但其中很少有含金属-碳σ键的金属有机化合物,本文首次报道了二茂铁鎓离子三氯乙酸盐和二氯二茂钛对DNA的断链作用。     

PHOTOLYSIS OF PHOSPHODIESTER BONDS IN PLASMID DNA BY HIGH INTENSITY UV LASER IRRADIATION

Abstract— The cleavage of phosphodiester bonds in DNA exposed to high intensity UV laser pulses in aerated aqueous solution has been investigated using a krypton fluoride excimer laser (248 nm) and bacterial plasmid DNA. The dependence of strand breakage on fluence and intensity has been studied in detail and shows that the process is non-linear with respect to intensity. The relationship between the quantum yield for strand breakage and intensity shows that the strand breakage reaction involves two-photon excitation of DNA bases. The quantum yield rises with intensity from a lower value of 7 times 10^-5 until a maximum value of 4.5 times 10^-4 is attained at intensities of 10¹¹ W m^-2 and above. This value is approximately fifty-fold higher than the quantum yield for strand breakage induced by exposure to low density UV irradiation (254 nm, 12 W m^-2). DNA sequencing experiments have shown that strand breakage occurs by the specific cleavage of the phosphodiester bond which lies immediately 3' to guanine residues in the DNA, leaving some alkali-labile remnant attached to the terminal phosphate. A mechanism for DNA strand breakage which involves the generation of guanine radical cations is proposed.     

Intelligent,Biodegradable, and Self‐Healing Hydrogels Utilizing DNA Quadruplexes

A new class of hydrogels utilizing DNA (DNA quadruplex gel) has been constructed by directly and symmetrically coupling deoxynucleotide phosphoramidite monomers to the ends of polyethylene glycols (PEGs) in liquid phase, and using the resulting DNA‐PEG‐DNA triblock copolymers as macromonomers. Elongation of merely four deoxyguanosine residues on PEG, which produces typically ≈10 grams of desired DNA‐PEG conjugates in one synthesis, resulted in intelligent and biodegradable hydrogels utilizing DNA quadruplex formation, which are responsive to various input signals such as Na⁺, K⁺, and complementary DNA strand. Gelation of DNA quadruplex gels takes place within a few seconds upon the addition of a trigger, enabling free formation just like Ca⁺‐alginate hydrogels or possible application as an injectable polymer (IP) gel. The obtained hydrogels show good thermal stability and rheological properties, and even display self‐healing ability.     

Complex Reconfiguration of DNA Nanostructures

Nucleic acids have been used to create diverse synthetic structural and dynamic systems. Toehold‐mediated strand displacement has enabled the construction of sophisticated circuits, motors, and molecular computers. Yet it remains challenging to demonstrate complex structural reconfiguration in which a structure changes from a starting shape to another arbitrarily prescribed shape. To address this challenge, we have developed a general structural‐reconfiguration method that utilizes the modularly interconnected architecture of single‐stranded DNA tile and brick structures. The removal of one component strand reveals a newly exposed toehold on a neighboring strand, thus enabling us to remove regions of connected component strands without the need to modify the strands with predesigned external toeholds. By using this method, we reconfigured a two‐dimensional rectangular DNA canvas into diverse prescribed shapes. We also used this method to reconfigure a three‐dimensional DNA cuboid.     

DNA zipper-based tweezers

Here we report the design and development of DNA zippers and tweezers. Essentially a zipper system consists of a normal strand (N), a weak strand (W), and an opening strand (O). N strand is made up of normal DNA bases, while W is engineered to have inosine substituting for guanine. By altering the number and order of inosine, W is engineered to provide less than natural bonding affinities to N in forming the [N:W] helix. When O is introduced (a natural complement of N), it competitively displaces W from [N:W] and forms [N:O]. This principle is incorporated in the development of a molecular device that can perform the functions of tweezers (sense, hold, and release). Tweezers were constructed by holding N and W together using a hinge at one end. Thus, when the tweezers open, N and W remain in the same vicinity. This allows the tweezers to cycle among open and close positions by their opening and closing strands. Control over their opening and closing kinetics is demonstrated. In contrast to the previously reported DNA tweezers, the zipper mechanism makes it possible to operate them with opening strands that do not contain single-stranded DNA overhangs. Our approach yields a robust, compact, and regenerative tweezer system that could potentially be integrated into complex nanomachines.     

The Relationship between DNA Sequences and Oligonucleotide‐Templated Silver Nanoclusters and Their Fluorescence Properties

A novel approach was developed to study the relationship between DNA sequences and DNA‐templated silver nanoclusters (DNA‐Ag NCs) in detail by using an ordinary DNA strand as an example. Three kinds of Ag NCs are formed by using the DNA strand as a scaffold. By dividing the DNA template into several parts according to their different affinities to Ag⁺, it was found that the fluorescence properties of DNA‐Ag NCs are related to not only the sequences but also to the position of different parts in the template, which provides a more efficient approach to obtain DNA‐Ag NCs with required photoluminescence properties and may ultimately contribute to the targeted synthesis of DNA‐Ag NCs.     

Isolation, characterization and expression of the complementary DNA for human tumor necrosis factor (TNF-alpha)

A cDNA for human TNF-alpha (615bp) was isolated by means of polymerase chain reaction (PCR) using first strand cDNA from PMA-induced HL-60 cells as template. The result from sequencing the 615 bp cDNA fragment indicated that it corresponded to the entire sequence of mature human TNF coding region. Direct expression of mature human TNF was achieved using a plasmid pHT-1 constructed by ligation of the cDNA and a synthetic DNA. The IPTG-induced bacterial product (hTNF) showed cytotoxicity to mouse L-929 cells. The TNF activity was further identified by neutralization of a specific monoclonal antibody against human TNF-alpha. Approximately 80,000 units of activity were detected per ml of culture at A600 = 2.