Characterizations for Some Types of DNA Graphs

Vertex induced subgraphs of directed de Bruijn graphs with labels of fixed length k and over α letter alphabet are (α,k)-labelled. DNA graphs are (4,k)-labelled graphs. Pendavingh et al. proved that it is NP-hard to determine the smallest value α _k (D) for which a directed graph D can be (α _k (D),k)-labelled for any fixed . In this paper, we obtain the following formulas: and for cycle C _n and path P _n . Accordingly, we show that both cycles and paths are DNA graphs. Next we prove that rooted trees and self-adjoint digraphs admit a (Δ,k)-labelling for some positive integer k and they are DNA graphs if and only if Δ ≤ 4, where Δ is the maximum number in all out-degrees and in-degrees of such digraphs.     

Improved Fluorometric DNA Determination Based on the Interaction of the DNA/Polycation Complex with Hoechst 33258

When DNA is mixed with the cationic polyelectrolyte poly(diallyldimethyl ammonium chloride) (PDDA), the DNA/PDDA complex is formed instantaneously at room temperature. This complex is much more efficient in enhancing the fluorescence of Hoechst 33258 (H 33258) than DNA alone. Based on the interaction of H 33258 with the DNA/PDDA complex, a new fluorescence assay for DNA is described. At pH 7.3 in Tris-HCl buffered solution, the DNA/PDDA complex causes a sharp enhancement in fluorescence intensity of H 33258. Simultanously, the emission maximum wavelength of H 33258 blueshifts from 490nm to 450nm, while the excitation redshifts from 345 to 350nm. The calibration graphs for calf thymus DNA (ctDNA) and herring sperm DNA (hsDNA) are both linear up to 5.0µgmL^–1 when the concentration of H 33258 and PDDA are fixed at 1.5×10^–6 and 1.6×10^–5molL^–1, respectively. The method is specific for native DNA. The 3 detection limits for ctDNA and hsDNA are 1.8 and 5.6ngmL^–1, respectively, i.e. much lower than in the presence of H 33258 alone. Four synthetic samples were determined satisfactorily. This method can also be developed to investigate the formation and the nature of the complexes between DNA and polycations, which have recently been widely applied in some fields such as genetic engineering and gene therapy.     

A Complete Solution to a Conjecture on the β-Polynomials of Graphs

In 1990, Gutman and Mizoguchi conjectured that all roots of the -polynomial (G,C,x) of a graph G are real. Since then, there has been some literature intending to solve this conjecture. However, in all existing literature, only classes of graphs were found to show that the conjecture is true; for example, monocyclic graphs, bicyclic graphs, graphs such that no two circuits share a common edge, graphs without 3-matchings, etc, supporting the conjecture in some sense. Yet, no complete solution has been given. In this paper, we show that the conjecture is true for all graphs, and therefore completely solve this conjecture.     

Self-assembled plasmid DNA network prepared through both triple-helix formation and streptavidin–biotin interaction

Plasmid DNA responds to external stimuli to change the degree of supercoiling. As a result of its unique topological change, plasmid DNA is considered to be a new functional material. In addition to its stimuli-responsiveness, plasmid DNA has the capability of forming a triple helix with a triple-helix-forming oligonucleotide (TFO). The triple helix is formed in aqueous conditions and arises through recognition of specific sequences, and may lead to the formation of supramolecular architectures. With this in mind, we analyze the self-assembly of recombinant plasmid DNA with two sequences for triple-helix formation and TFO by means of surface plasmon resonance. In addition, the network formed by self-assembly of the recombinant plasmid DNA with biotinated-TFO and streptavidin is prepared and evaluated by atomic force microscopy (AFM).

Schematic illustration of plasmid DNA network.     

The Fluorescent Reaction Between Quinaldine Red and Nucleic Acids and its Application to Fluorescent Assay of DNA and RNA

The reaction between quinaldine red (QR) and nucleic acids was studied. The free QR alone has no fluorescence in solution. However, it becomes fluorescent after binding to nucleic acids, giving maximum emission at 607nm with maximum excitation at 557nm. Maximum fluorescence intensity is produced in the pH range of 3.2–3.6. Based on the fluorescent reactions, a novel fluorometric method was developed for rapid determination of nucleic acids using QR as the fluorescent probe. Under optimal conditions, the calibration graphs were linear in the range of 0–30.0µgmL^–1 for CT DNA and 0–20.0µgmL^–1 for yeast RNA. The limits of detection were 38ngmL^–1 for CT DNA and 142ngmL^–1 for yeast RNA. Four synthetic samples were determined with satisfaction.Received December 20, 2002; accepted March 27, 2003 Published online August 8, 2003     

On the Ordering of a Class of Graphs with Respect to their Matching Numbers

Based on the number of k-matching m(G,k) of a graph G, Gutman and Zhang introduced an order relation of graphs: for graphs G ₁ and G ₂, if m(G ₁,k) ≥ m(G ₂,k) for all k. The order relation has important applications in comparing Hosaya indices and energies of molecular graphs and has been widely studied. Especially, Gutman and Zhang gave complete orders of six classes of graphs with respect to the relation . In this paper, we consider a class of graphs with special structure, which is a generalization of a class of graphs studied by Gutman and Zhang. Some order relations in the class of graphs are given, and the maximum and minimum elements with respect to the order relation are determined. The new results can be applied to order some classes of graphs by their matching numbers.     

One-milliliter wet-digestion for inductively coupled plasma mass spectrometry (ICP-MS): determination of platinum-DNA adducts in cells treated with platinum(II) complexes

Platinum (Pt)–DNA adducts formed by the anti-tumor agent cisplatin are recognized by the DNA mismatch repair (MMR) system. To investigate the involvement of MMR proteins including hMLH1 in the removal of these adducts, we developed a mL-scale wet-digestion method for inductively coupled plasma mass spectrometry (ICP-MS). The detection limit was 0.01 ng mL^–1 Pt, which corresponded to 2 pg Pt/g DNA when 10 g of DNA was used. The mean relative errors were 5.4% or better for a dynamic range of 0.01–10 ng mL^–1 Pt. DNA (~500 g) had no matrix effect. To improve the accuracy, DNA preparations were treated with ribonuclease and the apparent reduction in the concentration of Pt was corrected using cellular DNA levels, which were determined with Hoechst 33258. No significant differences were observed, in terms of the formation of Pt–DNA adducts or their removal over 6 h, between hMLH1-deficient HCT116 cells, a human colorectal cancer cell line, and hMLH1-complemented HCT116+ch3 cells (n=5; P>0.05), indicating that the hMLH1-dependent DNA repair systems contribute to neither the formation nor the removal of the adducts at detectable levels. In addition, approximately 19% of the adducts were removed within 6 h in both cell lines. A time course analysis (~24 h) suggested that the removal of cisplatin-generated Pt–DNA adducts follows first-order kinetics (t_1/2=32 h). The amount of Pt–DNA adduct formed by oxaliplatin in 1 h was 56% (ratio of means) of that generated by an equimolar concentration of cisplatin in HCT116. The proposed procedure could be useful for determining Pt–DNA adducts formed by Pt(II) complexes.     

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).

     

A Conjugated Polymer‐Based Electrochemical DNA Sensor: Design and Application of a Multi‐Functional and Water‐Soluble Conjugated Polymer

In this work, we report the design of a new multi‐functional, water‐soluble conjugated polymer integrating both a DNA intercalator and a redox label. Based on this multi‐functional conjugated polymer, we develop a sequence‐specific electrochemical DNA sensor, where the acridine unit serves as the basis for sequence discrimination, and the ferrocene label provides the electrochemical signal. Moreover, the conjugated polythiophene helps transfer electrons from ferrocene to the electrode. This sensor provides a new way for rapid and convenient detection of DNA targets.

     

The Hosoya index and the Merrifield–Simmons index

In this article, we give sharp bounds on the Hosoya index and the Merrifield–Simmons index for connected graphs of fixed size. As a consequence, we determine all connected graphs of any fixed order and size which maximize the Merrifield–Simmons index. Sharp lower bounds on the Hosoya index are known for graphs of order n and size \(m\in [n-1,2n-3]\cup \left( {n-1\atopwithdelims ()2},{n\atopwithdelims ()2}\right] \); while sharp upper bounds were only known for graphs of order n and size \(m\le n+2\). We give sharp upper bounds on the Hosoya index for dense graphs with \(m\ge {n\atopwithdelims ()2}-2n/3\). Moreover, all extreme graphs are also determined.     

Fluorescence‐Amplifying Assay for Irradiated DNA Lesions Using Water‐Soluble Conjugated Polymers

A new platform has been developed for DNA lesion detection using a cationic conjugated polymer (CCP). DNA that contains two adjacent thymine bases is irradiated with ultraviolet light to allow for the formation of cyclobutane pyrimidine dimers and pyrimidine–pyrimidone dimers. The DNA lesions block the primer extension, and the base labeled with fluorescein cannot be incorporated into the DNA strand. Addition of the CCP leads to inefficient fluorescence resonance energy transfer (FRET) from CCP to fluorescein. For the case without DNA lesions, successful primer extension allows for efficient FRET between them. In view of the FRET signal changes, the DNA lesions can be detected. This new protocol offers a convenient detection for DNA lesions in aqueous solution without any isolation and washing steps.

     

Responsive DNA‐Based Hydrogels and Their Applications

The term hydrogel describes a type of soft and wet material formed by cross‐linked hydrophilic polymers. The distinct feature of hydrogels is their ability to absorb a large amount of water and swell. The properties of a hydrogel are usually determined by the chemical properties of their constituent polymer(s). However, a group of hydrogels, called “smart hydrogels,” changes properties in response to environmental changes or external stimuli. Recently, DNA or DNA‐inspired responsive hydrogels have attracted considerable attention in construction of smart hydrogels because of the intrinsic advantages of DNA. As a biological polymer, DNA is hydrophilic, biocompatible, and highly programmable by Watson‐Crick base pairing. DNA can form a hydrogel by itself under certain conditions, and it can also be incorporated into synthetic polymers to form DNA‐hybrid hydrogels. Functional DNAs, such as aptamers and DNAzymes, provide additional molecular recognition capabilities and versatility. In this Review, DNA‐based hydrogels are discussed in terms of their stimulus response, as well as their applications.

     

Positively Charged Compact Quantum Dot–DNA Complexes for Detection of Nucleic Acids

Selective DNA detection: The fluorescence, from stable cationic QDs, is quenched by 90% on complexation with modified DNA molecules. The QD–DNA probe is capable of detecting pathogenic DNA fragments at concentrations as low as 200 nM in solution and shows selective fluorescence recovery in the presence of target DNA (see spectrum c in figure) vs noncomplementary DNA (spectrum d).

     

Spectrofluorimetric determination of nucleic acids as 8-hydroxyquinoline/ yttrium ternary complexes

The formation of nucleic acids/8-hydroxyquinoline/yttrium(III) ternary complexes and their fluorescent properties have been studied. The nucleic acids studied include native and thermally denatured calf thymus DNA, fish sperm DNA and yeast RNA. In the range of pH 7.6–8.5, controlled by NH₃-NH₄C1 buffer, ternary complexes are formed that fluoresce at different wavelengths with different nucleic acids. Based on the fluorescence reactions, sensitive spectrofluorimetric methods for nucleic acids are proposed. In optimal conditions, the calibration curves were linear in the range 0.5–4.0 gml^–1 for calf thymus DNA, 0.5–2.5 g ml^–1 for fish sperm DNA and 0.5–4.0 g ml^–1 for yeast RNA. The limits of determination (3 ) were 0.030 g ml^–1 for calf thymus DNA, 0.020 g ml^–1 for fish sperm DNA and 0.090 g ml^–1 for yeast RNA. Corresponding to the interferences of coexisting substances, six synthetic samples were constructed and the results of determination were satisfactory.     

Spectral change in X-ray absorption near edge structure of DNA thin films irradiated with monochromatic soft X-rays

To reveal the chemical changes induced in DNA by irradiation with ionizing radiation, we have investigated the spectral change in the X-ray absorption near edge structure (XANES) of DNA resulting from exposure to monochromatic soft X-rays. We used a thin film of calf thymus DNA as a sample and observed nitrogen K-shell and oxygen K-shell XANES spectra. The typical monochromatic soft X-ray energies used for the irradiation (395, 408, 528, and 538 eV) were obtained from a soft X-ray beamline (BL23SU, SPring-8). These energies correspond to those just below or just above the nitrogen and oxygen K-shell ionization energy, respectively. The obtained XANES spectra show significant changes by irradiation. Particularly a new π* resonance peak in oxygen XANES spectra evidently appeared by the irradiation above oxygen K-shell ionization potential. These results suggest that carbonyl groups, presumably a propenal group (OC–CC), may be produced in the sample by oxygen ionization. Thus characteristic damage induced by induction in the DNA molecule would be predicted following exposure to monochromatized synchrotron soft X-rays.     

Efficient Replication Bypass of Size‐Expanded DNA Base Pairs in Bacterial Cells

Supersize me! Size‐expanded DNA bases (xDNA) are able to encode natural DNA sequences in replication. In vitro experiments with a DNA polymerase show nucleotide incorporation opposite the xDNA bases with correct pairing. In vivo experiments using E. coli show that two xDNA bases (xA and xC, see picture) encode the correct replication partners.

     

Unicycle Graphs with Maximum Generalized Topological Indices

Let G be an unicycle graph and d _v the degree of the vertex v. In this paper, we investigate the following topological indices for an unicycle graph , , where m ≥ 2 is an integer. All unicycle graphs with the largest values of the three topological indices are characterized. This research is supported by the National Natural Science Foundation of China(10471037)and the Education Committee of Hunan Province(02C210)(04B047).