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• Journal article
  Sengar A, Vandana JJ, Chambers VS, Di Antonio M, Winnerdy FR, Balasubramanian S, Anh TPet al., 2019,

  Structure of a (3+1) hybrid G-quadruplex in the PARP1 promoter

  , NUCLEIC ACIDS RESEARCH, Vol: 47, Pages: 1564-1572, ISSN: 0305-1048
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  • Citations: 47
• Journal article
  Mao S-Q, Ghanbarian AT, Spiegel J, Cuesta SM, Beraldi D, Di Antonio M, Marsico G, Hansel-Hertsch R, Tannahill D, Balasubramanian Set al., 2018,

  DNA G-quadruplex structures mold the DNA methylome

  , Nature Structural and Molecular Biology, Vol: 25, Pages: 951-957, ISSN: 1545-9985

  Control of DNA methylation level is critical for gene regulation, and the factors that govern hypomethylation at CpG islands (CGIs) are still being uncovered. Here, we provide evidence that G-quadruplex (G4) DNA secondary structures are genomic features that influence methylation at CGIs. We show that the presence of G4 structure is tightly associated with CGI hypomethylation in the human genome. Surprisingly, we find that these G4 sites are enriched for DNA methyltransferase 1 (DNMT1) occupancy, which is consistent with our biophysical observations that DNMT1 exhibits higher binding affinity for G4s as compared to duplex, hemi-methylated, or single-stranded DNA. The biochemical assays also show that the G4 structure itself, rather than sequence, inhibits DNMT1 enzymatic activity. Based on these data, we propose that G4 formation sequesters DNMT1 thereby protecting certain CGIs from methylation and inhibiting local methylation.

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• Journal article
  Greenfield JL, Evans EW, Di Nuzzo D, Di Antonio M, Friend RH, Nitschke JRet al., 2018,

  Unraveling Mechanisms of Chiral Induction in Double-Helical Metallopolymers

  , Journal of the American Chemical Society, Vol: 140, Pages: 10344-10353, ISSN: 0002-7863

  © 2018 American Chemical Society. Self-assembled helical polymers hold great promise as new functional materials, where helical handedness controls useful properties such as circularly polarized light emission or electron spin. The technique of subcomponent self-assembly can generate helical polymers from readily prepared monomers. Here we present three distinct strategies for chiral induction in double-helical metallopolymers prepared via subcomponent self-assembly: (1) employing an enantiopure monomer, (2) polymerization in a chiral solvent, (3) using an enantiopure initiating group. Kinetic and thermodynamic models were developed to describe the polymer growth mechanisms and quantify the strength of chiral induction, respectively. We found the degree of chiral induction to vary as a function of polymer length. Ordered, rod-like aggregates more than 70 nm long were also observed in the solid state. Our findings provide a basis to choose the most suitable method of chiral induction based on length, regiochemical, and stereochemical requirements, allowing stereochemical control to be established in easily accessible ways.

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• Journal article
  Sahakyan AB, Chambers VS, Marsico G, Santner T, Di Antonio M, Balasubramanian Set al., 2017,

  Machine learning model for sequence-driven DNA G-quadruplex formation

  , SCIENTIFIC REPORTS, Vol: 7, ISSN: 2045-2322
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  • Citations: 109
• Journal article
  Hansel-Hertsch R, Di Antonio M, Balasubramanian S, 2017,

  DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential

  , NATURE REVIEWS MOLECULAR CELL BIOLOGY, Vol: 18, Pages: 279-284, ISSN: 1471-0072
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• Journal article
  Nieto-Orellana A, Di Antonio M, Conte C, Falcone FH, Bosquillon C, Childerhouse N, Mantovani G, Stolnik Set al., 2017,

  Effect of polymer topology on non-covalent polymer-protein complexation: miktoarm versus linear mPEG-poly(glutamic acid) copolymers

  , POLYMER CHEMISTRY, Vol: 8, Pages: 2210-2220, ISSN: 1759-9954
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• Journal article
  Xu H, Di Antonio M, McKinney S, Mathew V, Ho B, O'Neil NJ, Dos Santos N, Silvester J, Wei V, Garcia J, Kabeer F, Lai D, Soriano P, Banath J, Chiu DS, Yap D, Le DD, Ye FB, Zhang A, Thu K, Soong J, Lin S-C, Tsai AHC, Osako T, Algara T, Saunders DN, Wong J, Xian J, Bally MB, Brenton JD, Brown GW, Shah SP, Cescon D, Mak TW, Caldas C, Stirling PC, Hieter P, Balasubramanian S, Aparicio Set al., 2017,

  CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours

  , Nature Communications, Vol: 8, Pages: 1-18, ISSN: 2041-1723

  G-quadruplex DNAs form four-stranded helical structures and are proposed to play key roles in different cellular processes. Targeting G-quadruplex DNAs for cancer treatment is a very promising prospect. Here, we show that CX-5461 is a G-quadruplex stabilizer, with specific toxicity against BRCA deficiencies in cancer cells and polyclonal patient-derived xenograft models, including tumours resistant to PARP inhibition. Exposure to CX-5461, and its related drug CX-3543, blocks replication forks and induces ssDNA gaps or breaks. The BRCA and NHEJ pathways are required for the repair of CX-5461 and CX-3543-induced DNA damage and failure to do so leads to lethality. These data strengthen the concept of G4 targeting as a therapeutic approach, specifically for targeting HR and NHEJ deficient cancers and other tumours deficient for DNA damage repair. CX-5461 is now in advanced phase I clinical trial for patients with BRCA1/2 deficient tumours (Canadian trial, NCT02719977, opened May 2016).

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• Journal article
  Nicoli F, Roos MK, Hemmig EA, Di Antonio M, de Vivie-Riedle R, Liedl Tet al., 2016,

  Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes

  , JOURNAL OF PHYSICAL CHEMISTRY A, Vol: 120, Pages: 9941-9947, ISSN: 1089-5639
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• Journal article
  Hansel-Hertsch R, Beraldi D, Lensing SV, Marsico G, Zyner K, Parry A, Di Antonio M, Pike J, Kimura H, Narita M, Tannahill D, Balasubramanian Set al., 2016,

  G-quadruplex structures mark human regulatory chromatin

  , Nature Genetics, Vol: 48, Pages: 1267-1272, ISSN: 1061-4036

  G-quadruplex (G4) structural motifs have been linked to transcription1,2, replication3 and genome instability4,5 and are implicated in cancer and other diseases6,7,8. However, it is crucial to demonstrate the bona fide formation of G4 structures within an endogenous chromatin context9,10. Herein we address this through the development of G4 ChIP–seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. We find ∼10,000 G4 structures in human chromatin, predominantly in regulatory, nucleosome-depleted regions. G4 structures are enriched in the promoters and 5′ UTRs of highly transcribed genes, particularly in genes related to cancer and in somatic copy number amplifications, such as MYC. Strikingly, de novo and enhanced G4 formation are associated with increased transcriptional activity, as shown by HDAC inhibitor–induced chromatin relaxation and observed in immortalized as compared to normal cellular states. Our findings show that regulatory, nucleosome-depleted chromatin and elevated transcription shape the endogenous human G4 DNA landscape.

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• Journal article
  Chambers VS, Marsico G, Boutell JM, Di Antonio M, Smith GP, Balasubramanian Set al., 2015,

  High-throughput sequencing of DNA G-quadruplex structures in the human genome

  , Nature Biotechnology, Vol: 33, Pages: 877-881, ISSN: 1087-0156

  G-quadruplexes (G4s) are nucleic acid secondary structures that form within guanine-rich DNA or RNA sequences. G4 formation can affect chromatin architecture and gene regulation and has been associated with genomic instability, genetic diseases and cancer progression1,2,3,4. Here we present a high-resolution sequencing–based method to detect G4s in the human genome. We identified 716,310 distinct G4 structures, 451,646 of which were not predicted by computational methods5,6,7. These included previously uncharacterized noncanonical long loop and bulged structures8,9. We observed a high G4 density in functional regions, such as 5′ untranslated regions and splicing sites, as well as in genes previously not predicted to contain these structures (such as BRCA2). G4 formation was significantly associated with oncogenes, tumor suppressors and somatic copy number alterations related to cancer development10. The G4s identified in this study may therefore represent promising targets for cancer intervention.

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• Journal article
  Yangyuoru PM, DiAntonio M, Ghimire C, Biffi G, Balasubramanian S, Mao Het al., 2015,

  Dual Binding of an Antibody and a Small Molecule Increases the Stability of TERRA G‐Quadruplex

  , Angewandte Chemie, Vol: 127, Pages: 924-927, ISSN: 0044-8249

  <jats:title>Abstract</jats:title><jats:p>In investigating the binding interactions between the human telomeric RNA (TERRA) G‐quadruplex (GQ) and its ligands, it was found that the small molecule carboxypyridostatin (cPDS) and the GQ‐selective antibody BG4 simultaneously bind the TERRA GQ. We previously showed that the overall binding affinity of BG4 for RNA GQs is not significantly affected in the presence of cPDS. However, single‐molecule mechanical unfolding experiments revealed a population (48 %) with substantially increased mechanical and thermodynamic stability. Force‐jump kinetic investigations suggested competitive binding of cPDS and BG4 to the TERRA GQ. Following this, the two bound ligands slowly rearrange, thereby leading to the minor population with increased stability. Given the relevance of G‐quadruplexes in the regulation of biological processes, we anticipate that the unprecedented conformational rearrangement observed in the TERRA‐GQ–ligand complex may inspire new strategies for the selective stabilization of G‐quadruplexes in cells.</jats:p>

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• Journal article
  Yangyuoru PM, Di Antonio M, Ghimire C, Biffi G, Balasubramanian S, Mao Het al., 2015,

  Dual Binding of an Antibody and a Small Molecule Increases the Stability of TERRA G-Quadruplex

  , ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, Vol: 54, Pages: 910-913, ISSN: 1433-7851
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  • Citations: 28
• Journal article
  Le DD, Di Antonio M, Chan LKM, Balasubramanian Set al., 2015,

  G-quadruplex ligands exhibit differential G-tetrad selectivity

  , CHEMICAL COMMUNICATIONS, Vol: 51, Pages: 8048-8050, ISSN: 1359-7345
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  • Citations: 89
• Journal article
  Di Antonio M, McLuckie KIE, Balasubramanian S, 2014,

  Reprogramming the Mechanism of Action of Chlorambucil by Coupling to a G-Quadruplex Ligand

  , JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 136, Pages: 5860-5863, ISSN: 0002-7863
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  • Citations: 70
• Journal article
  Di Antonio M, 2014,

  Quinone Methides Generation: Applications in Chemical Biology

  , CURRENT ORGANIC CHEMISTRY, Vol: 18, Pages: 2-2, ISSN: 1385-2728
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  • Citations: 2
• Journal article
  Biffi G, Di Antonio M, Tannahill D, Balasubramanian Set al., 2014,

  Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells

  , NATURE CHEMISTRY, Vol: 6, Pages: 75-80, ISSN: 1755-4330
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  • Citations: 503
• Journal article
  McLuckie KIE, Di Antonio M, Zecchini H, Xian J, Caldas C, Krippendorff B-F, Tannahill D, Lowe C, Balasubramanian Set al., 2013,

  G-Quadruplex DNA as a Molecular Target for Induced Synthetic Lethality in Cancer Cells

  , JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 135, Pages: 9640-9643, ISSN: 0002-7863
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  • Citations: 124
• Journal article
  Mitchell T, Ramos-Montoya A, Di Antonio M, Murat P, Ohnmacht S, Micco M, Jurmeister S, Fryer L, Balasubramanian S, Neidle S, Neal DEet al., 2013,

  Downregulation of Androgen Receptor Transcription by Promoter G-Quadruplex Stabilization as a Potential Alternative Treatment for Castrate-Resistant Prostate Cancer

  , BIOCHEMISTRY, Vol: 52, Pages: 1429-1436, ISSN: 0006-2960
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  • Citations: 24
• Journal article
  Nikan M, Di Antonio M, Abecassis K, McLuckie K, Balasubramanian Set al., 2013,

  An Acetylene-Bridged 6,8-Purine Dimer as a Fluorescent Switch-On Probe for Parallel G-Quadruplexes

  , ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, Vol: 52, Pages: 1428-1431, ISSN: 1433-7851
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  • Citations: 46
• Journal article
  Murat P, Gormally MV, Sanders D, Di Antonio M, Balasubramanian Set al., 2013,

  Light-mediated <i>in cell</i> downregulation of G-quadruplex-containing genes using a photo-caged ligand

  , CHEMICAL COMMUNICATIONS, Vol: 49, Pages: 8453-8455, ISSN: 1359-7345
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  • Citations: 36
• Journal article
  Di Antonio M, Rodriguez R, Balasubramanian S, 2012,

  Experimental approaches to identify cellular G-quadruplex structures and functions

  , METHODS, Vol: 57, Pages: 84-92, ISSN: 1046-2023
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  • Citations: 42
• Journal article
  Doria F, Nadai M, Folini M, Di Antonio M, Germani L, Percivalle C, Sissi C, Zaffaroni N, Alcaro S, Artese A, Richter SN, Freccero Met al., 2012,

  Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures

  , ORGANIC & BIOMOLECULAR CHEMISTRY, Vol: 10, Pages: 2798-2806, ISSN: 1477-0520
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  • Citations: 93
• Journal article
  Mueller S, Sanders DA, Di Antonio M, Matsis S, Riou J-F, Rodriguez R, Balasubramanian Set al., 2012,

  Pyridostatin analogues promote telomere dysfunction and long-term growth inhibition in human cancer cells

  , ORGANIC & BIOMOLECULAR CHEMISTRY, Vol: 10, Pages: 6537-6546, ISSN: 1477-0520
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  • Citations: 121
• Journal article
  Di Antonio M, Biffi G, Mariani A, Raiber E-A, Rodriguez R, Balasubramanian Set al., 2012,

  Selective RNA Versus DNA G-Quadruplex Targeting by In Situ Click Chemistry

  , ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, Vol: 51, Pages: 11073-11078, ISSN: 1433-7851
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  • Citations: 150
• Journal article
  Nadai M, Doria F, Di Antonio M, Sattin G, Germani L, Percivalle C, Palumbo M, Richter SN, Freccero Met al., 2011,

  Naphthalene diimide scaffolds with dual reversible and covalent interaction properties towards G-quadruplex

  , BIOCHIMIE, Vol: 93, Pages: 1328-1340, ISSN: 0300-9084
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  • Citations: 84
• Journal article
  Percivalle C, La Rosa A, Verga D, Doria F, Mella M, Palumbo M, Di Antonio M, Freccero Met al., 2011,

  Quinone Methide Generation via Photoinduced Electron Transfer

  , JOURNAL OF ORGANIC CHEMISTRY, Vol: 76, Pages: 3096-3106, ISSN: 0022-3263
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  • Citations: 42
• Journal article
  Verga D, Nadai M, Doria F, Percivalle C, Di Antonio M, Palumbo M, Richter SN, Freccero Met al., 2010,

  Photogeneration and Reactivity of Naphthoquinone Methides as Purine Selective DNA Alkylating Agents

  , JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 132, Pages: 14625-14637, ISSN: 0002-7863
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  • Citations: 97
• Journal article
  Doria F, di Antonio M, Benotti M, Verga D, Freccero Met al., 2009,

  Substituted Heterocyclic Naphthalene Diimides with Unexpected Acidity. Synthesis, Properties, and Reactivity

  , JOURNAL OF ORGANIC CHEMISTRY, Vol: 74, Pages: 8616-8625, ISSN: 0022-3263
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  • Citations: 48
• Journal article
  Di Antonio M, Doria F, Richter SN, Bertipaglia C, Mella M, Sissi C, Palumbo M, Freccero Met al., 2009,

  Quinone Methides Tethered to Naphthalene Diimides as Selective G-Quadruplex Alkylating Agents

  , JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 131, Pages: 13132-13141, ISSN: 0002-7863
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  • Citations: 134
• Journal article
  Di Antonio M, Doria F, Mella M, Merli D, Profumo A, Freccero Met al., 2007,

  Novel naphthalene diimides as activatable precursors of bisalkylating agents, by reduction and base catalysis

  , JOURNAL OF ORGANIC CHEMISTRY, Vol: 72, Pages: 8354-8360, ISSN: 0022-3263
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  • Citations: 36

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