Dr Afaf El-Sagheer

Dr Afaf El-Sagheer

Academic visitor (2005-)

Afaf studied chemistry at Suez Canal University (Egypt). She did research for her PhD at Southampton University with Professor John Mellor then moved back to Egypt to become a lecturer. She was recently promoted to Professor at Suez University. Afaf is now working with Prof Tom Brown in Oxford investigating the applications of oligonucleotides in biology. Her current work is focused on the use of click chemistry to assemble novel modified DNA and RNA constructs and on new methods of DNA synthesis.

78 Papers

Template-directed oligonucleotide strand ligation, covalent intramolecular DNA circularization and catenation using click chemistry

R. Kumar, A. H. El-Sagheer, J. Tumpane, P. Lincoln, L. M. Wilhelmsson and T. Brown. J. Am. Chem. Soc. 129 (21), 6859-6864, 2007.

Synthesis of alkyne and azide modified Oligonucleotides and their cyclisation by the CuAAC (Click) Reaction

A. H. El-Sagheer and T. Brown. Curr. Protoc. Nucleic Acid Chem. 2008.

Synthesis, Serum Stability and Cell Uptake of Cyclic and Hairpin Decoy Oligonucleotides for TCF/LEF and GLI Transcription Factors

A. H. El-Sagheer and T. Brown. Int. J. Pept. Res. Ther. 14 (4), 367-372, 2008.

A very stable cyclic DNA miniduplex with just two base pairs

A. H. El-Sagheer, R. Kumar, S. Findlow, J. M. Werner, A. N. Lane and T. Brown. ChemBioChem 9 (1), 50-52, 2008.

Rapid and efficient DNA strand cross-linking by click chemistry

P. Kocalka, A. H. El-Sagheer and T. Brown. ChemBioChem 9 (8), 1280-1285, 2008.

DNA Polymorphism as an Origin of Adenine-Thymine Tract Length-Dependent Threading Intercalation Rate

P. Nordell, F. Westerlund, A. Reymer, A. H. El-Sagheer, T. Brown, B. Norden and P. Lincoln. J. Am. Chem. Soc. 130 (44), 14651-14658, 2008.

Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems

K. Borjesson, S. Preus, A. H. El-Sagheer, T. Brown, B. Albinsson and L. M. Wilhelmsson. J. Am. Chem. Soc. 131 (12), 4288-4293, 2009.

Synthesis and Polymerase Chain Reaction Amplification of DNA Strands Containing an Unnatural Triazole Linkage

A. H. El-Sagheer and T. Brown. J. Am. Chem. Soc. 131 (11), 3958-3964, 2009.

Click chemistry with DNA

A. H. El-Sagheer and T. Brown. Chem. Soc. Rev. 39 (4), 1388-1405, 2010.

Factors influencing hairpin oligonucleotide cyclization by the uncatalyzed alkyne-azide cycloaddition (AAC) reaction

A. H. El-Sagheer and T. Brown. Pure Appl. Chem. 82 (8), 1599-1607, 2010.

A new fixation strategy for addressable nano-network building blocks

E. P. Lundberg, A. H. El-Sagheer, P. Kocalka, L. M. Wilhelmsson, T. Brown and B. Norden. Chem. Commun. 46 (21), 3714-3716, 2010.

New strategy for the synthesis of chemically modified RNA constructs exemplified by hairpin and hammerhead ribozymes

A. H. El-Sagheer and T. Brown. Proc. Natl. Acad. Sci. U.S.A. 107 (35), 15329-15334, 2010.

Functionalized Nanostructures: Redox-Active Porphyrin Anchors for Supramolecular DNA Assemblies

K. Borjesson, J. Wiberg, A. H. El-Sagheer, T. Ljungdahl, J. Martensson, T. Brown, B. Norden and B. Albinsson. ACS Nano 4 (9), 5037–5046, 2010.

Rapid chemical ligation of oligonucleotides by the Diels–Alder reaction

A. H. El-Sagheer, V. V. Cheong and T. Brown. Org. Biomol. Chem. 9 (1), 232-235, 2011.

Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA

A. Dierckx, P. Diner, A. H. El-Sagheer, J. D. Kumar, T. Brown, M. Grotli and L. M. Wilhelmsson. Nucleic Acids Res. 39 (10), 4513-4524, 2011.

Improved synthesis of 5-hydroxymethyl-2'-deoxycytidine phosphoramidite using a 2'-deoxyuridine to 2'-deoxycytidine conversion without temporary protecting groups

A. S. Hansen, A. Thalhammer, A. H. El-Sagheer, T. Brown and C. J. Schofield. Bioorg. Med. Chem. Lett. 21 (4), 1181-1184, 2011.

Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation

A. Thalhammer, A. S. Hansen, A. H. El-Sagheer, T. Brown and C. J. Schofield. Chem. Commun. 47, 5325-5327, 2011.

Fast Copper-Free Click DNA Ligation by the Ring Strain Promoted Alkyne-Azide Cycloaddition Reaction

M. Shelbourne, X. Chen, T. Brown and A. H. El-Sagheer. Chem. Commun. 47, 6257-6259, 2011.

Biocompatible artificial DNA linker that is read through by DNA polymerases and is functional in Escherichia coli

A. H. El-Sagheer, A. P. Sanzone, R. Gao, A. Tavassoli and T. Brown. Proc. Natl. Acad. Sci. U.S.A. 108 (28), 11338-11343, 2011.

Efficient RNA synthesis by in vitro transcription of a triazole-modified DNA template

A. H. El-Sagheer and T. Brown. Chem. Commun. 47 (44), 12057-12058, 2011.

Structure and Dynamics of Triazole-Linked DNA: Biocompatibility Explained

A. Dallmann, A. H. El-Sagheer, L. Dehmel, C. Muegge, C. Griesinger, N. P. Ernsting and T. Brown. Chem. Eur. J. 17 (52), 14714-14717, 2011.

Click Nucleic Acid Ligation

A. H. El-Sagheer and T. Brown. Nucleic Acid Therapeutics (formerly Oligonucleotides) 21, A6, 2011.

Towards Dark Quencher Based Real Time DNA Sequencing

J. Hohlbein, L. Le Reste, O. Potapova, C. Joyce, A. H. El-Sagheer, T. Brown and A. N. Kapanidis. Biophys. J. 98 (3), 611a-612a, 2010.

Fixation of Self-Assembled DNA Nanostructures by Simultaneous Multicenter Click Chemistry

E. P. Lundberg, A. H. El-Sagheer, P. Kocalka, L. M. Wilhelmsson, T. Brown and B. Norden. Biophys. J. 98 (3), 658a, 2010.

The First All-Nucleobase Analog FRET Pair

S. Preus, K. Borjesson, K. Kilsa, A. H. El-Sagheer, T. Brown, B. Albinsson, L. M. Wilhelmsson. Biophys. J. 98 (3), 582, 2010.

Click Nucleic Acid Ligation: Applications in Biology and Nanotechnology

A. H. El-Sagheer and T. Brown. Acc. Chem. Res. 45 (8), 1258-1267, 2012.

Fast and efficient DNA crosslinking and multiple orthogonal labelling by copper-free click chemistry

M. Shelbourne, T. Brown Jr, A. H. El-Sagheer and T. Brown. Chem. Commun. 2012.

Assessing the biocompatibility of click-linked DNA in Escherichia coli

A. P. Sanzone, A. H. El-Sagheer, T. Brown and A. Tavassoli. Nucleic Acids Res. 2012.

Tension induces a base-paired overstretched DNA conformation

N. Bosaeus, A. H. El-Sagheer, T. Brown, S. B. Smith, B. Akerman, C. Bustamante and B. Norden. Proc. Natl. Acad. Sci. U.S.A. 109 (38), 15179-15184, 2012.

Kinetics of Diffusion-Controlled DNA Hybridization in Lipid Monolayer Films Determined by Single Molecule Fluorescence Spectroscopy

J. K. Hannestad, R. Brune, I. Czolkos, A. Jesorka, A. H. El-Sagheer, T. Brown, B. Albinsson and O. Orwar. ACS Nano 7 (1), 308-315, 2013.

The Structure of FemXWv in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNAAla to Peptidoglycan Precursors

M. Fonvielle, I. Li de La Sierra-Gallay, A. H. El-Sagheer, M. Lecerf, D. Patin, D. Mellal, C. Mayer, D. Blanot, N. Gale, T. Brown, H. van Tilbeurgh, M. Ethève-Quelquejeu and M. Arthur. Angew. Chem. Int. Ed. 52 (28), 7278-7281, 2013.

Solid phase click ligation for the synthesis of very long oligonucleotides

J. Qiu, A. H. El-Sagheer and T. Brown. Chem. Commun. 49, 6959-6961, 2013.

Copper-free click chemistry as an emerging tool for the programmed ligation of DNA-functionalised gold nanoparticles

A. Heuer-Jungemann, R. Kirkwood, A. H. El-Sagheer, T. Brown and A. G. Kanaras. Nanoscale 2013.

Combined nucleobase and backbone modifications enhance DNA duplex stability and preserve biocompatibility

A. H. El-Sagheer and T. Brown. Chem. Sci. 5, 253-259, 2014.

Structural insights into how 5-hydroxymethylation influences transcription factor binding

L. Lercher, M. A. McDonough, A. H. El-Sagheer, A. Thalhammer, S. Kriaucionis, T. Brown and C. J. Schofield. Chem. Commun. 50, 1794-1796, 2014.

Transcription of Click-Linked DNA in Human Cells

C. N. Birts, A. P. Sanzone, A. H. El-Sagheer, J. P. Blaydes, T. Brown and A. Tavassoli. Angew. Chem. Int. Ed. 53 (9), 2362-2365, 2014.

Force-induced melting of DNA—evidence for peeling and internal melting from force spectra on short synthetic duplex sequences

N. Bosaeus, A. H. El-Sagheer, T. Brown, B. Akerman and B. Norden. Nucleic Acids Res. 42 (12), 8083-8091, 2014.

Reverse transcription through a bulky triazole linkage in RNA: implications for RNA sequencing

X. Chen, A. H. El-Sagheer and T. Brown. Chem. Commun. 50, 7597-7600, 2014.

Enzymatic Incorporation and Fluorescent Labelling of Cyclooctyne-Modified Deoxyuridine Triphosphates in DNA

X. Ren, M. Gerowska, A. H. El-Sagheer and T. Brown. Bioorg. Med. Chem. 2014.

Highly Sensitive DNA Sensor Based on Upconversion Nanoparticles and Graphene Oxide

P. Alonso-Cristobal, P. Vilela, A. H. El-Sagheer, E. Lopez-Cabarcos, T. Brown, O. L. Muskens, J. Rubio-Retama and A. G. Kanaras. ACS Appl. Mater. Interfaces 2015.

Azide and trans-Cyclooctene dUTPs: Incorporation into DNA Probes and Fluorescent Click-Labelling

T. Brown, X. Ren and A. H. El-Sagheer. Analyst 2015.

Click DNA and RNA ligation for new biocompatible nucleic acid backbone mimics

A. H. El-Sagheer and T. Brown. Collect. Czech. Chem. Commun. 12, 10-17, 2011.

A triazole linkage that mimics the DNA phosphodiester group in living systems

A. H. El-Sagheer and T. Brown. Q. Rev. Biophys 48 (4), 429-436, 2015.

Reversible Ligation of Programmed DNA-Gold Nanoparticle Assemblies

P. K. Harimech, S. R. Gerrard, A. H. El-Sagheer, T. Brown and A. G. Kanaras. J. Am. Chem. Soc. 137 (29), 9242-9245, 2015.

Programming the assembly of gold nanoparticles on graphene oxide sheets using DNA

A. Heuer-Jungemann, L. Kiessling, E. Stratakis, E. Kymakis, A. H. El-Sagheer, T. Brown and A. G. Kanaras. J. Mater. Chem. C 3, 9379-9384, 2015.

New Technologies for DNA analysis-A review of the READNA Project

S. McGinn, D. Bauer, T. Brefort, L. Dong, A. H. El-Sagheer, A. Elsharawy, G. Evans, E. Falk-Sorqvist, M. Forster, S. Fredriksson, P. Freeman, C. Freitag, J. Fritzsche, S. Gibson, M. Gullberg, M. Gut, S. Heath, I. Heath-Brun, A. J. Heron, J. Hohlbein, R. Ke, O. Lancaster, L. Le Reste, G. Maglia, R. Marie, F. Mauger, F. Mertes, M. Mignardi, L. Moens, J. Oostmeijer, R. Out, J. N. Pedersen, F. Persson, V. Picaud, D. Rotem, N. Schracke, J. Sengenes, P. F. Stahler, B. Stade, D. Stoddart, X. Teng, C. D. Veal, N. Zahra, H. Bayley, M. Beier, T. Brown, C. Dekker, B. Ekstrom, H. Flyvbjerg, A. Franke, S. Guenther, A. N. Kapanidis, J. Kaye, A. Kristensen, H. Lehrach, J. Mangion, S. Sauer, E. Schyns, J. Tost, J. M. L. M. van Helvoort, P. J. van der Zaag, J. O. Tegenfeldt, A. J. Brookes, K. Mir, M. Nilsson, S. Willcocks and I. G. Gut. N. Biotechnol. 33 (3), 311-330, 2016.

Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes

X. Ren, A. H. El-Sagheer and T. Brown. Nucleic Acids Res. 2016.

Stable End-Sealed DNA as Robust Nano-rulers for In Vivo Single-Molecule Fluorescence

A. Plochowietz, A. H. El-Sagheer, T. Brown and A. N. Kapanidis. Chem. Sci. 2016.

An autonomous molecular assembler for programmable chemical synthesis

W. Meng, R. A. Muscat, M. L. McKee, P. J. Milnes, A. H. El-Sagheer, J. Bath, B. G. Davis, T. Brown, R. K. O'Reilly and A. J. Turberfield. Nat. Chem. 2016.

Combination probes with intercalating anchors and proximal fluorophores for DNA and RNA detection

J. Qiu, A. Wilson, A. H. El-Sagheer and T. Brown. Nucleic Acids Res. 2016.

2'-Alkynylnucleotides: A Sequence- and Spin Label-Flexible Strategy for EPR Spectroscopy in DNA

M. M. Haugland, A. H. El-Sagheer, R. J. Porter, J. Pena, T. Brown, E. A. Anderson and J. E. Lovett. J. Am. Chem. Soc. 2016.

Selective killing of cells triggered by their mRNA signature in the presence of smart nanoparticles

A. Heuer-Jungemann, A. H. El-Sagheer, P. M. Lackie, T. Brown and A. G. Kanaras. Nanoscale 8, 16857-16861, 2016.

Electrophilic RNA for Peptidyl-RNA Synthesis and Site-Specific Cross-Linking with tRNA-Binding Enzymes

M. Fonvielle, N. Sakkas, L. Iannazzo, C. Le Fournis, D. Patin, D. Mengin-Lecreulx, A. H. El-Sagheer, E. Braud, S. Cardon, T. Brown, M. Arthur and M. Etheve-Quelquejeu. Angew. Chem. Int. Ed. 55 (43), 13553-13557, 2016.

Graphene Oxide-Upconversion Nanoparticle Based Optical Sensors for Targeted Detection of mRNA Biomarkers Present in Alzheimer’s Disease and Prostate Cancer

P. Vilela, A. H. El-Sagheer, T. M. Millar, T. Brown, O. L. Muskens and A. G. Kanaras. ACS Sensors 2 (1), 52-56, 2017.

Molecular Requirements of High-Fidelity Replication-Competent DNA Backbones for Orthogonal Chemical Ligation

A. Shivalingam, A. E. S. Tyburn, A. H. El-Sagheer and T. Brown. J. Am. Chem. Soc. 139 (4), 1575-1583, 2017.

5-Formylcytosine does not change the global structure of DNA

J. S Hardwick, D. Ptchelkine, A. H. El-Sagheer, I. Tear, D. Singleton, S. E. V. Phillips, A. N. Lane and T. Brown. Nat. Struct. Mol. Biol. 24, 544-552, 2017.

RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks

U. B. Abdullah, J. F. McGouran, S. Brolih, D. Ptchelkine, A. H. El-Sagheer, T. Brown and P. J. McHugh. EMBO J. 36, 2047-2060, 2017.

Towards complete sequence flexibility of nucleic acid base analogue FRET

M. S. Wranne, A. F. Füchtbauer, B. Dumat, M. Bood, A. H. El-Sagheer, T. Brown, H. Gradén, M. Grøtli and L. M. Wilhelmsson. J. Am. Chem. Soc. 139 (27), 9271-9280, 2017.

Instrument-free quantitative gold nanoparticle-based liquid-phase colorimetric assays for use in resource-poor environments

H. Wang, Y. Zhang, R. Li, J. Nie, A. H. El-Sagheer, T. Brown, Z. Liu and W. Xiao. Chem. Commun. 53, 8407-8410, 2017.

Site-selective immobilization of functionalized DNA origami on nanopatterned Teflon AF

M. Shaali, J. G. Woller, P. G. Johansson, J. K. Hannestad, L. de Battice, N. Aissaoui, T. Brown, A. H. El-Sagheer, S. Kubatkin, S. Lara-Avila, B. Albinsson and A. Jesorka. J. Mater. Chem. C 5, 7637-7643, 2017.

The Sedimentation of Colloidal Nanoparticles in Solution and Its Study Using Quantitative Digital Photography

J. Midelet, A. H. El-Sagheer, T. Brown, A. G. Kanaras and M. H. V. Werts. Part. Part. Syst. Char. 2017.

Locked nucleic acid (LNA) enhances binding affinity of triazole-linked DNA towards RNA

P. Kumar, A. H. El-Sagheer, L. Truong and T. Brown. Chem. Commun. 53, 8910-8913, 2017.

Assembly of a biocompatible triazole-linked gene by one-pot click-DNA ligation

M. Kukwikila, N. Gale, A. H. El-Sagheer, T. Brown and A. Tavassoli. Nat. Chem. 9, 1089-1098, 2017.

Single tube gene synthesis by phosphoramidate chemical ligation

A. H. El-Sagheer and T. Brown. Chem. Commun. 53, 10700-10702, 2017.

Searching for avidity by chemical ligation of combinatorially self-assembled DNA-encoded ligand libraries

S. Matysiak, K. Hellmuth, A. H. El-Sagheer, A. Shivalingam, Y. Ariyurek, M. de Jong, M. J. Hollestelle, R. Out and T. Brown. Org. Biomol. Chem. 16, 48-52, 2018.

Pentacyclic adenine: a versatile and exceptionally bright fluorescent DNA base analogue

M. Bood, A. F. Fuchtbauer, M. S. Wranne, J. J. Ro, S. Sarangamath, A. H. El-Sagheer, D. L. M. Rupert, R. S. Fisher, S. W. Magennis, A. C. Jones, F. Hook, T. Brown, B. H. Kim, A. Dahleni, L. M. Wilhelmsson and M. Grotli. Chem. Sci. 2018.

Redox Capacitive Assaying of C-Reactive Protein at a Peptide Supported Aptamer Interface

J. Piccoli, R. Hein, A. H. El-Sagheer, T. Brown, E. M. Cilli, P. R. Bueno and J. J. Davis. Anal. Chem. 90 (5), 3005-3008, 2018.

Sensing of Vimentin mRNA in 2D and 3D Models of Wounded Skin Using DNA-Coated Gold Nanoparticles

P. Vilela, A. Heuer-Jungemann, A. H. El-Sagheer, T. Brown, O. L. Muskens, N. R. Smyth and A. G. Kanaras. Small 2018.

Spectroscopic and Hydrodynamic Characterisation of DNA-Linked Gold Nanoparticle Dimers in Solution using Two-Photon Photoluminescence

J. Midelet, A. H. El-Sagheer, T. Brown, A. G. Kanaras, A. Debarre and M. H. V. Werts. ChemPhysChem 2018.

Multiplexed mRNA Sensing and Combinatorial-Targeted Drug Delivery Using DNA-Gold Nanoparticle Dimers

M. Kyriazi, D. Giust, A. H. El-Sagheer, P. M. Lackie, O. L. Muskens, T. Brown and A. G. Kanaras. ACS Nano 2018.

Gene assembly via one-pot chemical ligation of DNA promoted by DNA nanostructures

I. Manuguerra, S. Croce, A. H. El-Sagheer, A. Krissanaprasit, T. Brown, K. V. Gothelf and A. Manetto. Chem. Commun. 2018.

Graphene Oxide-Upconversion Nanoparticle Based Portable Sensors for Assessing Nutritional Deficiencies in Crops

D. Giust, M. I. Lucio, A. H. El-Sagheer, T. Brown, L. E. Williams, O. L. Muskens and A. G. Kanaras. ACS Nano 12 (6), 6273-6279, 2018.

Replication Fork Reversal during DNA Interstrand Crosslink Repair Requires CMG Unloading

R. Amunugama, S. Willcox, R. A. Wu, U. B. Abdullah, A. H. El-Sagheer, T. Brown, P. J. McHugh, J. D. Griffith and J. C. Walter. Cell Reports 23, 3419-3428, 2018.

Synthesis, Affinity for Complementary RNA and DNA, and Enzymatic Stability of Triazole-Linked Locked Nucleic Acids (t-LNAs).

P. Kumar, L. Truong Y. R. Baker, A. H. El-Sagheer and T. Brown. ACS Omega 3 (6), 6976-6987, 2018.

Preparation and characterization of manganese, cobalt and zinc DNA nanoflowers with tuneable morphology, DNA content and size

Y. R. Baker, J. Chen, J. Brown, A. H. El-Sagheer, P. Wiseman, E. Johnson, P. Goddard and T. Brown. Nucleic Acids Res. 46 (15), 7495-7505, 2018.

Fluorogenic thiazole orange TOTFO probes stabilise parallel DNA triplexes at pH 7 and above

S. Walsh, A. H. El-Sagheer and T. Brown. Chem. Sci. 2018.

Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation

J. Chen, Y. R. Baker, A. Brown, A. H. El-Sagheer and T. Brown. Chem. Sci. 2018.

Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue

C. P. Lawson, A. F. Fuchtbauer, M. S. Wranne, T. Giraud, T. Floyd, B. Dumat, N. K. Andersen, A. H. El-Sagheer, T. Brown, H. Graden, L. M. Wilhelmsson and M. Grotli. Sci. Rep. 2018.