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  • 1. Barken, K. B.
    et al.
    Gabig-Ciminska, Magdalena
    KTH, Tidigare Institutioner, Bioteknologi.
    Holmgren, Anders
    KTH, Tidigare Institutioner, Bioteknologi.
    Molin, S.
    Effect of unlabeled helper probes on detection of an RNA target by bead-based sandwich hybridization2004Inngår i: BioTechniques, ISSN 0736-6205, E-ISSN 1940-9818, Vol. 36, nr 1, s. 124-+Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Unlabeled helper oligonucleotides assisting a bead-based sandwich hybridization assay were tested for the optimal placement of the capture and detection probes. The target used was a full-length in vitro synthesized mRNA molecule. Helper probes complementary to regions adjacent to the binding site of the 5' end attached capture probe were found much more effective than helper probes targeting positions adjacent to the detection probe binding site. The difference is believed to be caused by a disruption of the RNA secondary structure in the area where the capture probe binds, thereby reducing structural interference from the bead. The use of additional helpers showed an additive effect. Using helpers, at both sides of the capture and detection probes showed a 15- to 40-fold increase in hybridization efficiency depending on the target, thereby increasing the sensitivity of the hybridization assays. Using an electrical chip linked to the detection probe for the detection of p-ominophenol, which is produced by alkaline phosphatase, a detection limit of 2 x 10(-13) M mRNA molecules was reached without the use of a nucleic acid amplification step.

  • 2.
    Gabig-Ciminska, Magdalena
    et al.
    KTH, Tidigare Institutioner, Bioteknologi.
    Holmgren, Anders
    KTH, Tidigare Institutioner, Bioteknologi.
    Andresen, Heiko
    KTH, Tidigare Institutioner, Bioteknologi.
    Barken, K. B.
    Wumpelmann, M.
    Albers, J.
    Hintsche, R.
    Breitenstein, A.
    Neubauer, P.
    Los, M.
    Czyz, A.
    Wegrzyn, G.
    Silfversparre, G.
    Jurgen, B.
    Schweder, T.
    Enfors, Sven-Olof
    KTH, Tidigare Institutioner, Bioteknologi.
    Electric chips for rapid detection and quantification of nucleic acids2004Inngår i: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 19, nr 6, s. 537-546Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A silicon chip-based electric detector coupled to bead-based sandwich hybridization (BBSH) is presented as an approach to perform rapid analysis of specific nucleic acids. A microfluidic platform incorporating paramagnetic beads with immobilized capture probes is used for the biorecognition steps. The protocol involves simultaneous sandwich hybridization of a single-stranded nucleic acid target with the capture probe on the beads and with a detection probe in the reaction solution, followed by enzyme labeling of the detection probe, enzymatic reaction, and finally, potentiometric measurement of the enzyme product at the chip surface. Anti-DIG-alkaline phosphatase conjugate was used for the enzyme labeling of the DIG-labeled detection probe. p-Aminophenol phosphate (pAPP) was used as a substrate. The enzyme reaction product, p-aminophenol (pAP), is oxidized at the anode of the chip to quinoneimine that is reduced back to pAP at the cathode. The cycling oxidation and reduction of these compounds result in a current producing a characteristic signal that can be related to the concentration of the analyte. The performance of the different steps in the assay was characterized using in vitro synthesized RNA oligonucleotides and then the instrument was used for analysis of 16S rRNA in Escherichia coli extract. The assay time depends on the sensitivity required. Artificial RNA target and 16S rRNA, in amounts ranging from 10(11) to 10(10) molecules, were assayed within 25 min and 4 h, respectively.

  • 3.
    Gabig-Ciminska, Magdalena
    et al.
    KTH, Tidigare Institutioner, Bioteknologi.
    Los, M.
    Holmgren, Anders
    KTH, Tidigare Institutioner, Fiber- och polymerteknologi.
    Albers, J.
    Czyz, A.
    Hintsche, R.
    Wegrzyn, G.
    Enfors, Sven-Olof
    KTH, Tidigare Institutioner, Bioteknologi.
    Detection of bacteriophage infection and prophage induction in bacterial cultures by means of electric DNA chips2004Inngår i: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 324, nr 1, s. 84-91Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Infections of bacterial cultures by bacteriophages are common and serious problems in many biotechnological laboratories and factories. A method for specific, quantitative, and quick detection of phage contamination, based on the use of electric DNA chip is described here. Different phages of Escherichia coli and Bacillus subtilis were analyzed. Phage DNA was isolated from bacterial culture samples and detected by combination of bead-based sandwich hybridization with enzyme-labeled probes and detection of the enzymatic product using silicon chips. The assay resulted in specific signals from all four tested phages without significant background. Although high sensitivity was achieved in 4h assay time, a useful level of sensitivity (10(7)-10(8) phages) is achievable within 25 min. A multiplex DNA chip technique involving a mixture of probes allows for detection of various types of phages in one sample.. These analyses confirmed the specificity of the assay.

  • 4.
    Holmgren, Anders
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Biochemical Control Aspects in Lignin Polymerization2008Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Lignins are produced by all vascular plants and they represent one of the most abundant groups of biopolymers in nature. Lignin chemistry research, which has been of great importance for the progress of pulping technologies, has been plagued by the difficulties of its isolation and characterization. The pioneering work of Karl Freudenberg in the 1950’s with synthetic models of lignin paved the way for a detailed structural characterization of many lignin substructures. His work with the so-called “synthetic lignins” or dehydrogenative polymers (DHP) also laid a foundation for understanding how different lignin substructures are formed, reinforcing the already existing theory of lignin polymerization. However, subsequent structural characterizations of DHPs and lignins have repeatedly put this theory to the test. In the past decade, even a new radically different hypothesis for lignin polymerization has emerged and is sustained by a few researchers in the field.

    In this work, DHPs were produced from phenolic monomers, mostly coniferyl alcohol, a common lignin monomer, in a variety of reaction conditions. This was done in order to establish how different chemical factors, potentially active in the plant cell wall during lignin polymerization, influence the polymer’s final properties. In the presence of nicotine amide adenine dinucleotide (NADH), a quinone methide model, which is an intermediate formed during lignin polymerization, was effectively reduced. An equivalent reduced structure was produced during DHP synthesis in the presence of NADH. These studies showed that reduction might take place during oxidative polymerization, possibly explaining how reduced lignin structures are formed in the plant cell wall. Another reductive agent, ascorbic acid, was also tested during synthesis of DHPs. It displayed a totally different effect than NADH, probably due to its anti-oxidant nature, by altering the final amounts of certain inter-unit substructures, in favour of β-O-4′ structures, which are so prominent in natural lignins. Furthermore, the new suggested model for lignin polymerization, stating that lignin itself possesses the ability for template replication, was tested by synthesizing DHPs in the presence of a simple β-β′ substructure model. The DHPs produced the same amounts of β-β′ substructures as a control synthesis without the model structure, indicating that no replication had occurred. Finally, the role of the monolignol γ-carbon oxidation state in lignin polymerization, was studied. Hypothetically, lignin- like polymers could be produced by the plant, using monolignol biosynthetic precursors which exhibit γ-carbonyl groups instead of an alcohol group, like the common lignin monomer. Synthetic lignins produced with ferulic acid, coniferaldehyde and the normal monolignol, coniferyl alcohol, displayed important differences in chemical and physical properties. Both the ferulic acid and coniferaldehyde polymers exhibited almost no saturated inter-unit substructures and very few cyclic structures, both of which are very common in coniferyl alcohol dehydrogenative polymers and natural lignins. This could have significant implications for the formation of an important type of lignin carbohydrate complexes (LCC). Also the hydrophobicity of the alcohol-type polymer was lower than the other two. The biological implications of all these findings are discussed and some suggestions are made to explain how all these factors might affect lignin polymerization and structure in nature.

  • 5.
    Holmgren, Anders
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Brunow, Gösta
    Department of Chemistry, University of Helsinki.
    Henriksson, Gunnar
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Zhang, Liming
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Ralph, John
    US Dairy Forage Research Center, USDA-Agricultural Research Service.
    Non-enzymatic reduction of quinone methides during oxidative coupling of monolignols: implications for the origin of benzyl structures in lignins2006Inngår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 4, nr 18, s. 3456-3461Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lignin is believed to be synthesized by oxidative coupling of 4-hydroxyphenylpropanoids. In native lignin there are some types of reduced structures that cannot be explained solely by oxidative coupling. In the present work we showed via biomimetic model experiments that nicotinamide adenine dinucleotide ( NADH), in an uncatalyzed process, reduced a beta-aryl ether quinone methide to its benzyl derivative. A number of other biologically significant reductants, including the enzyme cellobiose dehydrogenase, failed to produce the reduced structures. Synthetic dehydrogenation polymers of coniferyl alcohol synthesized ( under oxidative conditions) in the presence of the reductant NADH produced the same kind of reduced structures as in the model experiment, demonstrating that oxidative and reductive processes can occur in the same environment, and that reduction of the in situ-generated quinone methides was sufficiently competitive with water addition. In situ reduction of beta - beta-quinone methides was not achieved in this study. The origin of racemic benzyl structures in lignins therefore remains unknown, but the potential for simple chemical reduction is demonstrated here.

  • 6.
    Holmgren, Anders
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Henriksson, Gunnar
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Zhang, Liming
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Effects of a Biologically Relevant Antioxidant on the Dehydrogenative Polymerization of Coniferyl Alcohol2008Inngår i: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 9, nr 12, s. 3378-3382Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dehydrogenation polymers (DHPs or synthetic lignins) were synthesized from coniferyl alcohol by enzymatic oxidation in the presence of ascorbic acid to study the potential effects of an antioxidant upon their structure. Specific interunit substructures (beta-O-4', beta-beta', and beta-5') were quantified by C-13 NMR, which showed how ascorbic acid altered their amounts compared with control syntheses without this antioxidant, especially by increasing the amount of beta-O-4' substructures. The effect of ascorbic acid increased with its concentration. Surprisingly, no influence on the sizes of the synthetic lignins, as determined by size exclusion chromatography, was observed. The chemistry of this antioxidant effect during dehydrogenative polymerization and the potential biological significance (cell wall lignification) of these observations are discussed.

  • 7.
    Holmgren, Anders
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Norgren, Magnus
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Fiberteknologi.
    Zhang, Liming
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Henriksson, Gunnar
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    On the role of the monolignol gamma-carbon functionality in lignin biopolymerization2009Inngår i: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700, Vol. 70, nr 1, s. 147-155Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In order to investigate the importance of the monomeric gamma-carbon chemistry in lignin biopolymerization and structure, synthetic lignins (dehydrogenation polymers; DHP) were made from monomers with different degrees of oxidation at the gamma-carbon, i.e., carboxylic acid, aldehyde and alcohol. All monomers formed a polymeric material through enzymatic oxidation. The polymers displayed similar sizes by size exclusion chromatography analyses, but also exhibited some physical and chemical differences. The DHP made of coniferaldehyde had poorer solubility properties than the other DHPs, and through contact angle of water measurement on spin-coated surfaces of the polymeric materials, the DHPs made of coniferaldehyde and carboxylic ferulic acid exhibited higher hydrophobicity than the coniferyl alcohol DHP. A structural characterization with C-13 NMR revealed major differences between the coniferyl alcohol-based polymer and the coniferaldehyde/ferulic acid polymers, such as the predominance of aliphatic double bonds and the lack of certain benzylic structures in the latter cases. The biological role of the reduction at the gamma-carbon during monolignol biosynthesis with regard to lignin polymerization is discussed.

  • 8.
    Holmgren, Anders
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik.
    Zhang, Liming
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik.
    Brunow, G.
    Henriksson, Gunnar
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik.
    Origin of reduced lignin structures: Quinone methides2005Inngår i: Appita Annu. Conf., 2005, s. 147-150Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Recent discoveries have shown the presence of reduced lignin structures in softwood lignin, such as dihydroconiferyl alcohol and secoisolariciresinol. During lignin polymerization, the oxidative radical coupling of monolignols generates quinone methides as intermediates. Several reduction agents were tested on a quinone methide model. The products were analyzed by GC-MS and 1H, 13C, DEPT and HSQC NMR techniques were used to confirm the structure of the reduced quinone methide. An uncatalyzed reduction of this quinone methide model was achieved with β-NADH, a biologically significant reducing agent, demonstrating that the formation of reduced lignin structures is not necessarily biologically controlled.

  • 9.
    Holmgren, Anders
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Zhang, Liming
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Brunow, Gösta
    Helsingfors Universitet.
    Henriksson, Gunnar
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Origin of reduced structures: Quinomethids2005Inngår i: 13th ISWFPC V3, 2005, s. 147-150Konferansepaper (Annet (populærvitenskap, debatt, mm))
  • 10.
    Holmgren, Anders
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Zhang, Liming
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Henriksson, Gunnar
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    In vitro monolignol dehydrogenative polymerization in the presence of a candidate dimer template modelManuskript (Annet vitenskapelig)
  • 11.
    Holmgren, Anders
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Zhang, Liming
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Henriksson, Gunnar
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknik, Träkemi och massateknologi.
    Monolignol dehydrogenative polymerization in vitro in the presence of dioxane and a methylated beta-beta ' dimer model compound2008Inngår i: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 62, nr 5, s. 508-513Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lignin formation is believed to occur by polymerization of resonance-stabilized monolignol radicals formed by enzymatic oxidation. Recently, different hypotheses suggested that lignin polymerization is influenced by surfaces in the cell wall which can be polysaccharides or proteins. The latter is called the proteinaceous dirigent sites/template polymerization hypothesis. According to another hypothesis, lignin itself is believed to act as a template and replicate its primary structure. In this work, dehydrogenative polymerization (DHP) of the lignin precursor coniferyl alcohol was performed in vitro in the presence and absence of pinoresinol dimethyl ether (a beta-beta ' dimer model). Another peculiarity of the experiments was the presence of dioxane which afforded a high solubility of the reactants. The question was whether the presence of beta-beta ' dimer model would change the structure of the DHP formed. The DHPs were analyzed by quantitative C-13 NMR, GC-FID, and GC-MS. The dimer model as a template in the homogeneous polymerization state (in solution) did not influence the DHP structure.

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