Dr Afaf El-Sagheer

Dr Afaf El-Sagheer

Academic visitor (2005-)

Afaf did rher PhD at Southampton University with Professor John Mellor then moved back to Egypt to become Professor of Chemistry at Suez University. Afaf has been working with Prof Tom Brown in Southampton and Oxford since 2005, focusing on the applications of oligonucleotides in biology. Her current work is on the use of click chemistry to assemble novel modified DNA and RNA constructs with artificial biocompatible backbones, and on oligonucleotide-based therapeutics and gene editing.She has published mor than 100 papers. In 2023 Afaf became an Assistant Professor in CVhemistry at Southampton University and continues to collaborate with the Brown group.

127 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.

CRISPRi is not strand-specific and redefines the transcriptional landscape

F. S. Howe, A. Russell, A. El-Sagheer, A. Nair, T. Brown and J. Mellor. eLife 6, 29878, 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 19 (7), 827-836, 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. 54, 4529-4532, 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. 9, 7681-7687, 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. 9, 8110-8120, 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. 8, 2018.

Squaramide-Based 5'-Phosphate Replacements Bind to the DNA Repair Exonuclease SNM1A

E. Dürr, W. Doherty, S. Y. Lee, A. H. El-Sagheer, A. Shivalingam, P. J. McHugh, T. Brown and J. F. McGouran. ChemistrySelect 3 (45), 12824-12829, 2018.

DNA-Coated Gold Nanoparticles for the Detection of mRNA in Live Hydra Vulgaris Animals

M. Moros, M. Kyriazi, A. H. El-Sagheer, T. Brown, C. Tortiglione and A. G. Kanaras. ACS Appl. Mater. Interfaces 11 (15), 13905-13911, 2018.

Synthesis of Lipid-Carbohydrate-Peptidyl-RNA Conjugates to Explore the Limits Imposed by the Substrate Specificity of Cell Wall Enzymes on the Acquisition of Drug Resistance

M. Fonvielle, A. Bouhss, C. Hoareau, D. Patin, D. Mengin-Lecreulx, L. Iannazzo, N. Sakkas, A. H. El-Sagheer, T. Brown, M. Etheve-Quelquejeu and M. Arthur. Chem. Eur. J. 24 (56), 14911-14915, 2018.

An artificial triazole backbone linkage provides a split-and-click strategy to bioactive chemically modified CRISPR sgRNA

L. Taemaitree, A. Shivalingam, A. H. El-Sagheer and T. Brown. Nat. Commun. 10, 2019.

Synthesis and biophysical properties of carbamate-locked nucleic acid (LNA) oligonucleotides with potential antisense applications

C. Thorpe, S. Epple, B. Woods, A. H. El-Sagheer and T. Brown. Org. Biomol. Chem. 17, 5341-5348, 2019.

Design of thiazole orange oligonucleotide probes for detection of DNA and RNA by fluorescence and duplex melting

P. Klimkowski, S. De Ornellas, D. Singleton, A. H. El-Sagheer and T. Brown. Org. Biomol. Chem. 17, 5943-5950, 2019.

NMR analyses on N-hydroxymethylated nucleobases - implications for formaldehyde toxicity and nucleic acid demethylases

S. Shishodia, D. Zhang, A. H. El-Sagheer, T. Brown, T. D. W. Claridge, C. J. Schofield and R. J. Hopkinson. Org. Biomol. Chem. 16 (21), 4021-4032, 2018.

Radiolabeled oligonucleotides targeting the RNA subunit of telomerase inhibit telomerase and induce DNA damage in telomerase-positive cancer cells

M. R. Jackson, B. M. Bavelaar, P. A. Waghorn, M. R. Gill, A. H. El-Sagheer, T. Brown, M. Tarsounas and K. A. Vallis. Cancer Res. 2019.

Optimised oligonucleotide substrates to assay XPF ERCC1 nuclease activity for the discovery of DNA repair inhibitors

A. M. Thomas, S. Brolih, J. F. McGouran, A. H. El-Sagheer, D. Ptchelkine, M. Jones P. J. McHugh and T. Brown. Chem. Commun. 55 (78), 11671-11674, 2019.

Light-induced reversible DNA ligation of gold nanoparticle superlattices.

De Fazio, A. F.; El-Sagheer, A. H.; Kahn, J. S.; Nandhakumar, I.; Burton, M. R.; Brown, T.; Muskens, O. L.; Gang, O.; Kanaras, A. G.. ACS Nano 13 (5), 5771-5777, 2019.

Optimising DNA-Coated Gold Nanoparticles to Enrich Skeletal Stem Cells from Human Bone Marrow Samples.

Lanham, S.; Xavier, M.; Kyriazi, M.; Alexaki, K.; El-Sagheer, A.; Brown, T.; Kanaras, A.; Oreffo, R. O. C.. biorvix 2019.

DNA-Coated Gold Nanoparticles for the Detection of mRNA in Live Hydra Vulgaris Animals.

36. Moros, M.; Kyriazi, M.-E.; El-Sagheer, A. H.; Brown, T.; Tortiglione, C.; Kanaras, A. G.. ACS Applied Materials & Interfaces 11 (15), 13905-13911, 2019.

Structure of the ?-globin locus through in vivo erythroid differentiation with extreme spatial and temporal resolution.

Oudelaar, A. M.; Beagrie, R. A.; Gosden, M.; de Ornellas, S.; Georgiades, E.; Kerry, J.; Hidalgo, D.; Carrelha, J.; Shivalingam, A.; El-Sagheer, A. H.; Telenius, J. M.; Brown, T.; Buckle, V. J.; Socolovsky, M.; Higgs, D. R.; Hughes, J. R.. biorvix 763763, 2019.

An artificial triazole backbone linkage provides a split-and-click strategy to bioactive chemically modified CRISPR sgRNA.

Taemaitree, L.; Shivalingam, A.; El-Sagheer, A. H.; Brown, T.. Nature Communications 10 (1), 1610, 2019.

“Split-and-Click” sgRNA

Lapatrada Taemaitree, Arun Shivalingam, Afaf H. El-Sagheer, Tom Brown. Methods in molecular biology 2162, 61-78, 2019.

Light-Induced Reversible DNA Ligation of Gold Nanoparticle Superlattices

Angela F. De Fazio, Afaf H. El-Sagheer, Jason S. Kahn, Iris Nandhakumar, Matthew Richard Burton, Tom Brown, Otto L. Muskens, Oleg Gang*, and Antonios G. Kanaras*. ACS Nano 13 (5), 5771-5777, 2019.

Oxidative DNA Cleavage with Clip-Phenanthroline Triplex-Forming Oligonucleotide Hybrids

Alessandro Panattoni, Afaf H. El-Sagheer, Tom Brown, Andrew Kellett, Michal Hocek. ChemBioChem 21, 991-1000, 2020.

Lighting Up DNA with the Environment-Sensitive Bright Adenine Analogue qAN4

Anders F. Füchtbauer, Moa S. Wranne, Sangamesh Sarangamath, Mattias Bood, Afaf H. El-Sagheer, Tom Brown, Henrik Gradén, Morten Grøtli, L. Marcus Wilhelmsson. ChemPlusChem 85 (2), 319-326, 2020.

Searching for the ideal triazole: Investigating the 1,5-triazole as a charge neutral DNA backbone mimic

Ysobel R. Baker, Diallo Traoré, Przemyslaw Wanat, Agnès Tyburn, Afaf H. El-Sagheer, TomBrown. Tetrahedron 76 (7), 130914, 2020.

Squaramides and Ureas: A Flexible Approach to Polymerase-Compatible Nucleic Acid Assembly

Arun Shivalingam, Lapatrada Taemaitree, Afaf H. El-Sagheer, Tom Brown. Angew. Chem. Int. Ed. 59 (28), 11416-11422, 2020.

Molecular flexibility of DNA as a key determinant of RAD51 recruitment

Federico Paoletti, Afaf H El-Sagheer, Jun Allard, Tom Brown, Omer Dushek, Fumiko Esashi. The EMBO Journal 39 (7), 2020.

2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis

Jack S Hardwick, Marius M Haugland, Afaf H El-Sagheer, Denis Ptchelkine, Frank R Beierlein, Andrew N Lane, Tom Brown, Janet E Lovett, Edward A Anderson. Nucleic Acids Res. 48 (6), 2830-2840, 2020.

Consecutive 5'- and 3'-amide linkages stabilise antisense oligonucleotides and elicit an efficient RNase H response

Sven Epple, Cameron Thorpe, Ysobel R. Baker, Afaf H. El-Sagheer, Tom Brown. Chemical Communications 56, 5496-5499, 2020.

Dynamics of the 4D genome during in vivo lineage specification and differentiation

A. Marieke Oudelaar, Robert A. Beagrie, Matthew Gosden, Sara de Ornellas, Emily Georgiades, Jon Kerry, Daniel Hidalgo, Joana Carrelha, Arun Shivalingam, Afaf H. El-Sagheer, Jelena M. Telenius, Tom Brown, Veronica J. Buckle, Merav Socolovsky, Douglas R. Higgs & Jim R. Hughes . Nature Communications 11, 2722, 2020.

Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor

Anna Wypijewska del Nogal, Anders F Füchtbauer, Mattias Bood, Jesper R Nilsson, Moa S Wranne, Sangamesh Sarangamath, Pauline Pfeiffer, Vinoth Sundar Rajan, Afaf H El-Sagheer, Anders Dahlén, Tom Brown, Morten Grøtli, L Marcus Wilhelmsson. Nucleic Acids Res. 48 (14), 7640-7652, 2020.

An 111In-labelled bis-ruthenium(ii) dipyridophenazine theranostic complex: mismatch DNA binding and selective radiotoxicity towards MMR-deficient cancer cells

Martin R. Gill, Michael G. Walker, Sarah Able, Ole Tietz, Abirami Lakshminarayanan, Rachel Anderson, Rod Chalk, Afaf H. El-Sagheer, Tom Brown, Jim A. Thomas and Katherine A. Vallis. Chemical Science 11, 8936-8944, 2020.

Development of Gene-Targeted Polypyridyl Triplex-Forming Oligonucleotide Hybrids

Nicolò Zuin Fantoni, Bríonna McGorman, Zara Molphy, Daniel Singleton, Sarah Walsh, Afaf H. El-Sagheer, Vickie McKee, Tom Brown, Andrew Kellett. ChemBioChem 21 (24), 3563-3574, 2020.

A DNA sensor based on upconversion nanoparticles and two-dimensional dichalcogenide materials

Konstantina Alexaki, Davide Giust, Maria-Eleni Kyriazi, Afaf H. El-Sagheer, Tom Brown, Otto L. Muskens & Antonios G. Kanaras. Frontiers of Chemical Science and Engineering 15, 935-943, 2021.

High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale

Damien J. Downes, Robert A. Beagrie, Matthew E. Gosden, Jelena Telenius, Stephanie J. Carpenter, Lea Nussbaum, Sara De Ornellas, Martin Sergeant, Chris Q. Eijsbouts, Ron Schwessinger, Jon Kerry, Nigel Roberts, Arun Shivalingam, Afaf El-Sagheer, A. Marieke Oudelaar, Tom Brown, Veronica J. Buckle, James O. J. Davies & Jim R. Hughes. Nature Communications 12, 531, 2021.

Enrichment of Skeletal Stem Cells from Human Bone Marrow Using Spherical Nucleic Acids

Miguel Xavier, Maria-Eleni Kyriazi, Stuart Lanham, Konstantina Alexaki, Elloise Matthews, Afaf H. El-Sagheer, Tom Brown, Antonios G. Kanaras*, and Richard O. C. Oreffo*. ACS Nano 15 (4), 6909-6916, 2021.

DNA Gold Nanoparticle Motors Demonstrate Processive Motion with Bursts of Speed Up to 50 nm Per Second

Alisina Bazrafshan, Maria-Eleni Kyriazi, Brandon Alexander Holt, Wenxiao Deng, Selma Piranej, Hanquan Su, Yuesong Hu, Afaf H. El-Sagheer, Tom Brown, Gabriel A. Kwong, Antonios G. Kanaras, and Khalid Salaita*. ACS Nano 15 (5), 8427-8438, 2021.

A Hitchhiker’s Guide to Click-Chemistry with Nucleic Acids

Nicolò Zuin Fantoni, Afaf H. El-Sagheer, and Tom Brown*. Chemical Reviews 121 (12), 7122-7154, 2021.

Artificial nucleic acid backbones and their applications in therapeutics, synthetic biology and biotechnology

Sven Epple, Afaf H. El-Sagheer, Tom Brown. Energing topics in life science 5 (5), 691-697, 2021.

Expanding the chemical functionality of DNA nanomaterials generated by rolling circle amplification

Ysobel R Baker, Liyiwen Yuan, Jinfeng Chen, Roman Belle, Robert Carlisle, Afaf H El-Sagheer, Tom Brown. Nucleic Acids Res. 49 (16), 9042-9052, 2021.

A New 1,5-Disubstituted Triazole DNA Backbone Mimic with Enhanced Polymerase Compatibility

Sven Epple, Aman Modi, Ysobel R. Baker, Ewa Wegrzyn, Diallo Traoré, Przemyslaw Wanat, Agnes E. S. Tyburn, Arun Shivalingam, Lapatrada Taemaitree, Afaf H. El-Sagheer, and Tom Brown*. Journal of the American Chemical Society 143 (39), 16293-16301, 2021.

Structure-Based Design of Selective Fat Mass and Obesity Associated Protein (FTO) Inhibitors

Shifali Shishodia, Marina Demetriades, Dong Zhang, Nok Yin Tam, Pratheesh Maheswaran, Caitlin Clunie-O’Connor, Anthony Tumber, Ivanhoe K. H. Leung, Yi Min Ng, Thomas M. Leissing, Afaf H. El-Sagheer, Eidarus Salah, Tom Brown, Wei Shen Aik*, Michael A. McDonough*, and Christopher J. Schofield*. Journal of Medical Chemistry 64 (22), 16609-16625, 2021.

Deoxyribonucleic Acid Encoded and Size-Defined pi-Stacking of Perylene Diimides

Jeffrey Gorman, Sarah R. E. Orsborne, Akshay Sridhar, Raj Pandya, Peter Budden, Alexander Ohmann, Naitik A. Panjwani, Yun Liu, Jake L. Greenfield, Simon Dowland, Victor Gray, Seán T. J. Ryan, Sara De Ornellas, Afaf H. El-Sagheer, Tom Brown, Jonathan R. Nitschke, Jan Behrends, Ulrich F. Keyser, Akshay Rao, Rosana Collepardo-Guevara, Eugen Stulz, Richard H. Friend*, and Florian Auras*. Journal of the American Chemical Society 144 (1), 368-376, 2022.

An Investigation into the Resistance of Spherical Nucleic Acids against DNA Enzymatic Degradation

Maria-Eleni Kyriazi, Afaf H. El-Sagheer, Igor L. Medintz, Tom Brown, and Antonios G. Kanaras*. Bioconjugate Chem. 33 (1), 219-225, 2022.

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

Johanna Midelet, Afaf H. El-Sagheer, Tom Brown, Antonios G. Kanaras, Anne Débarre, Martinus H. V. Werts. ChemPhysChem 19 (7), 827-836, 2018.

Short-Read Single-Molecule DNA Sequencing for Highly Parallel Analysis of Protein-DNA Interactions

Rebecca Andrews, Horst Steuer, Arun Shivalingam, Afaf H. El-Sagheer, Tom Brown, Achillefs N. Kapanidis. Biophysical Journal 114 (3), 2018.

Transient DNA binding to gapped DNA substrates links DNA sequence to the single-molecule kinetics of protein-DNA interactions

Rebecca Andrews, Horst Steuer, Afaf H El-Sagheer, Abhishek Mazumder, Hafez el Sayyed, Arun Shivalingam, Tom Brown, Achillefs N Kapanidis. bioRxiv 0 (0), 2022.

Enzymatic Synthesis of Chemical Nuclease Triplex-Forming Oligonucleotides with Gene-Silencing Applications

Brionna McGorman, Nicolo Zuin Fantoni , Sinead O’Carroll , Anna Ziemele, Afaf H. El-Sagheer, Tom Brown and Andrew Kellett. Nucleic Acids Research 50, 5467-5487, 2022.

Covalently attached intercalators restore duplex stability and splice-switching activity to triazole-modified oligonucleotides

Anna Dysko, Ysobel R. Baker, Graham McClorey, Matthew J. A. Wood, Sabine Fenner, Glynn Williams, Afaf El-Sagheer and Tom Brown. RSC Chemical Biology 3, 765-772, 2022.

An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides

Ysobel Baker, Cameron Thorpe, Jinfeng Chen, Laura Poller, Lina Cox, Pawan Kumar, Wooi Fang Lim, Lillian Lie, Graham McClorey, Sven Epple, Daniel Singleton, Michael McDonough, Jack Hardwick, Kirsten Christensen, Matthew Wood, James Hall, Afaf El-Sagheer, Tom Brown. Nature Communications 13 (1), 1-11, 2022.

A new phosphoramidite enables orthogonal double labelling to form combination oligonucleotide probes

Chunsen Bai, Piotr Klimkowski, Cheng Jin, Jagannath Kuchlyan, Afaf H. El-Sagheer* and Tom Brown*. Org. Biomol. Chem. 20, 8618-8622, 2022.

Synthesis and Properties of Oligonucleotides Containing LNA-Sulfamate and Sulfamide Backbone Linkages

Belma Zengin Kurt, Debashis Dhara, Afaf H. El-Sagheer and Tom Brown. Org. Lett 26 (19), 4137-4141, 2024.

Modular and Automated Synthesis of Oligonucleotide-Small Molecule Conjugates for Cathepsin B Mediated Traceless Release of Payloads

Cheng Jin, Siqi Li, Katherine A. Vallis, Afaf H. El-Sagheer and Tom Brown. RSC Chemical Biology 5, 738-744, 2024.

Synthesis, Biophysical and Biological Evaluation of Splice-Switching Oligonucleotides with Multiple LNA-Phosphothiotriester Backbones

Dhara, Debashis; Hill, Alyssa; Ramesh, Abinaya; Wood, Matthew; El-Sagheer, Afaf; Brown, Tom.. Journal of the American Chemical Society 146, 29773-29781, 2024.