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  • 1.
    Araújo, Ana Catarina
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Nakhai, Azadeh
    KTH, School of Biotechnology (BIO), Glycoscience.
    Ruda, M.
    Slättegård, R.
    Gatenholm, P.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    A general route to xyloglucan-peptide conjugates for the activation of cellulose surfaces2012In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 354, p. 116-120Article in journal (Refereed)
    Abstract [en]

    Cellulose is an attractive supporting matrix for diverse biotechnological applications, including chromatography, diagnostics, and tissue replacement/scaffolding, due to its renewable resource status, low cost, and low non-specific interaction with biomolecules. In an effort to expand the biofunctionality of cellulose materials, we present here a versatile method for the synthesis of xyloglucan-peptide conjugates that harness the strong xyloglucan-cellulose binding interaction for gentle surface modification. Xylogluco-oligosaccharide aminoalditols (XGO-NH 2) were coupled to both linear and cyclic peptides, which contained the endothelial cell epitope Arg-Gly-Asp, in a facile two-step approach employing diethyl squarate cross-linking. Subsequent xyloglucan endo-transglycosylase-mediated coupling of the resulting XGO-GRGDS (Gly-Arg-Gly-Asp-Ser) and XGO-c[RGDfK]-PEG-PEG (cyclo[Arg-Gly-Asp-(d-Phe)-Lys]-PEG-PEG; where PEG is 8-amino-3,6-dioxaoctanoic acid) conjugates into high molecular mass xyloglucan yielded xyloglucan-RGD peptide conjugates suitable for cellulose surface activation. Notably, use of XGO-squaramate as a readily accessible, versatile intermediate overcomes previous limitations of solid-phase synthetic approaches to XGO-peptide conjugates, and furthermore allows the method to be generalized to a wide variety of polypeptides and proteins, as well as diverse primary amino compounds.

  • 2.
    Araújo, Ana Catarina
    et al.
    Univ Lisbon, Lisbon, Portugal .
    Rauter, Amelia P.
    Nicotra, Francesco
    Airoldi, Cristina
    Costa, Barbara
    Cipolla, Laura
    Sugar-Based Enantiomeric and Conformationally Constrained Pyrrolo[2,1-c][1,4]-Benzodiazepines as Potential GABA(A) Ligands2011In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 54, no 5, p. 1266-1275Article in journal (Refereed)
    Abstract [en]

    Synthesis of a library of pyrrolo[2,1-c][1,4]-benzodiazepines derived from spiro bicyclic D- or L-proline analogues containing a D- or L-fructose moiety was developed. The L-fructose moiety was obtained by using a new synthetic pathway starting from L-arabinose through a six steps synthesis in 18% overall yield. Molecular modeling calculations and DNMR studies showed that D- and L.-fructose-based pyrrolobenzodiazepines exhibit a rigid (P)- and (M)-helical conformation, respectively, in which the C-11a substituent was always pseudoequatorial. Additionally, pyrrolobenzodiazepines functionalized with a chloride, bromide, nitro, or amino group in the benzene ring, with or without N-methylation and with or without protection of sugar alcohol groups, allowed a relationship between the molecular structure and biological activity to be established. The conformation of the diazepam ring was not the sole key player influencing binding affinities, and the sugar moiety can in some cases increase the binding activity, possibly by compounds have increased the understanding of the differential recognition receptor. participating in the binding event. Finally, these of (M)-/(P)-helical benzodiazepines on GABA(A) receptor.

  • 3.
    Araújo, Ana Catarina
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Song, Yajing
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ståhl, Patrik L.
    Brumer, Harry, III
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Activated Paper Surfaces for the Rapid Hybridization of DNA through Capillary Transport2012In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 84, no 7, p. 3311-3317Article in journal (Refereed)
    Abstract [en]

    The development of low-cost, accurate, and equipment-free diagnostic tests is crucial to many clinical, laboratory, and field applications, including forensics and medical diagnostics. Cellulose fiber-based paper is an inexpensive, biodegradable, and renewable resource, the use of which as a biomolecule detection matrix and support confers several advantages compared to traditional materials such as glass. In this context, a new, facile method for the preparation of surface functionalized papers bearing single-stranded probe DNA (ssDNA) for rapid target hybridization via capillary transport is presented. Optimized reaction conditions were developed that allowed the direct, one-step activation of standard laboratory filters by the inexpensive and readily available bifunctional linking reagent, 1,4-phenylenediisothiocyanate. Such papers were thus amenable to subsequent coupling of amine-labeled ssDNA under standard conditions widely used for glass-based supports. The intrinsic wicking ability of the paper matrix facilitated rapid sample elution through arrays of probe DNA, leading to significant, detectable hybridization in the time required for the sample liquid to transit the vertical length of the strip (less than 2 min). The broad applicability of these paper test strips as rapid and specific diagnostics in "real-life" situations was exemplified by the discrimination of amplicons generated from canine and human mitochondrial and genomic DNA in mock forensic samples.

  • 4.
    Song, Yajing
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gyarmati, Péter
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Araújo, Ana Catarina
    KTH, School of Biotechnology (BIO), Glycoscience.
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brumer, Harry, III
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Ståhl, Patrik L.
    Visual detection of DNA on paper chips2014In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 86, no 3, p. 1575-1582Article in journal (Refereed)
    Abstract [en]

    On-site DNA analysis for diagnostic or forensic purposes is much anticipated in the future of molecular testing. Yet the challenges to achieve this goal remain large with rapid and inexpensive detection and visualization being key factors for any portable analysis system. We have developed a filter paper-based nucleic acid assay, which is able to identify and distinguish dog and human genomic and mitochondrial samples in a forensic setting. The filter paper material allows for transport by capillary force of the sample DNA through the detection surface, allowing the targets to hybridize specifically to their complementary capture sequences. Coupling micrometer-sized beads to DNA allows the results to be visualized by the naked eye, enabling instant, cost-efficient, and on-site detection, while eliminating the need for advanced expensive instrumentation.

  • 5.
    Thongpoo, Preeyanuch
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    McKee, Lauren S.
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Araújo, Ana Catarina
    KTH, School of Biotechnology (BIO), Glycoscience.
    Kongsaeree, Prachumporn T.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Identification of the acid/base catalyst of a glycoside hydrolase family 3 (GH3) beta-glucosidase from Aspergillus niger ASKU282013In: Biochimica et Biophysica Acta - General Subjects, ISSN 0304-4165, E-ISSN 1872-8006, Vol. 1830, no 3, p. 2739-2749Article in journal (Refereed)
    Abstract [en]

    Background: The commercially important glycoside hydrolase family 3 (GH3) beta-glucosidases from Aspergillus niger are anomeric-configuration-retaining enzymes that operate through the canonical double-displacement glycosidase mechanism. Whereas the catalytic nucleophile is readily identified across all GH3 members by sequence alignments, the acid/base catalyst in this family is phylogenetically variable and less readily divined. Methods: In this report, we employed three-dimensional structure homology modeling and detailed kinetic analysis of site-directed mutants to identify the catalytic acid/base of a GH3 beta-glucosidase from A. niger ASKU28. Results: In comparison to the wild-type enzyme and other mutants, the E490A variant exhibited greatly reduced k(cat) and k(cat)/K-m values toward the natural substrate cellobiose (67,000- and 61,000-fold, respectively). Correspondingly smaller kinetic effects were observed for artificial chromogenic substrates p-nitrophenyl beta-D-glucoside and 2,4-dinitrophenyl beta-D-glucoside, the aglycone leaving groups of which are less dependent on add catalysis, although changes in the rate-determining catalytic step were revealed for both, pH-rate profile analyses also implicated E490 as the general acid/base catalyst. Addition of azide as an exogenous nucleophile partially rescued the activity of the E490A variant with the aryl beta-glucosides and yielded beta-glucosyl azide as a product. Conclusions and general significance: These results strongly support the assignment of E490 as the acid/base catalyst in a beta-glucosidase from A. niger ASKU28, and provide crucial experimental support for the bioinformatic identification of the homologous residue in a range of related GH3 subfamily members.

  • 6.
    Xu, Chunlin
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Spadiut, Oliver
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Araujo, Ana Catarina
    KTH, School of Biotechnology (BIO), Glycoscience.
    Nakhai, Azadeh
    KTH, School of Biotechnology (BIO), Glycoscience.
    Willfor, Stefan
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Chemo-enzymatic assembly of clickable cellulose surfaces via multivalent polysaccharides2012In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 243Article in journal (Other academic)
  • 7.
    Xu, Chunlin
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Spadiut, Oliver
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Araújo, Ana Catarina
    KTH, School of Biotechnology (BIO).
    Nakhai, Azadeh
    KTH, School of Biotechnology (BIO), Glycoscience.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Chemo-enzymatic Assembly of Clickable Cellulose Surfaces via Multivalent Polysaccharides2012In: ChemSusChem, ISSN 1864-5631, Vol. 5, no 4, p. 661-665Article in journal (Refereed)
    Abstract [en]

    The chemist′s guide to the galactosyl unit: A chemo-enzymatic process is developed for the multivalent functionalization of cellulose surfaces via regioselective oxidation of heteropolysaccharides with galactose 6-oxidase. Reductive amination, surface sorption, and click chemistry enable the assembly of (bio)chemically active cellulose surfaces for applications ranging from functional biocomposites to in vitro diagnostics.

1 - 7 of 7
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