2011 – 2020 papers


Selective Chemical Functionalization at N6-Methyladenosine Residues in DNA Enabled by Visible-Light-Mediated Photoredox Catalysis

M Nappi, A Hofer, S Balasubramanian and M Gaunt
J. Am. Chem. Soc., 2020, 21484-21492
DOI: 10.1021/jacs.0c10616


Activation-induced cytidine deaminase localizes to G-quadruplex motifs at mutation hotspots in lymphoma

Y-Z Xu, P Jenjaroenpun, T Wongsurawat, S D Byrum, V Shponka, D Tannahill, E AnChavez, S S Hung, C Steidl, S Balasubramanian, L M Rimsza and S Kendrick
NAR Cancer, 2020, 2:4, zcaa029
DOI: 10.1093/narcan/zcaa029


Natural, modified DNA bases

M Bilyard, S Becker and S Balasubramanian
Currently. Op. in Chemistry. Bio., 2022, 57, 1-7
DOI: 10.1016/j.cbpa.2020.01.014


Landscape of G-quadruplex DNA structural regions in breast cancer

R Hänsel-Hertsch, A Simeone, A Shea, W Hui, K Zyner, G Marsico, O Rueda, A Bruna, A Martin, X Zhang, S Adhikari, D Tannahill, C Caldas and S Balasubramanian
Nature Genetics, 2020, 52, 878-883
DOI: 10.1038/s41588-020-0672-8


Single-molecule visualization of DNA G-quadruplex formation in live cells

M Di Antonio, A Ponjavic, A Radzevičius, R T Ranasinghe, M Catalano, X Zhang, J Shen, L-M Needham, S F Lee, D Klenerman and S Balasubramanian
Nature Chemistry, 2020, 12, 832–837
DOI: 10.1038/s41557-020-0506-4


Genome-wide DNA Methylation Signatures Are Determined by DNMT3A/B Sequence Preferences

S-Q Mao, S Martinez Cuesta, D Tannahill and S Balasubramanian
Biochemistry, 2020, 59, 27, 2541–2550
DOI: 10.1021/acs.biochem.0c00339


The regulation and functions of DNA and RNA G-quadruplexes

D Varshney, J Spiegel, K Zyner, D Tannahill and S Balasubramanian
Nature Reviews Molecular Cell Biology, 2020, 21, 459–474
DOI: 10.1038/s41580-020-0236-x


Affinity-selected bicyclic peptide G-quadruplex ligands mimic a protein-like binding mechanism

K C Liu, K Röder, C Mayer, S Adhikari, D J Wales and S Balasubramanian
J. Am. Chem. Soc.2020, 142, 18, 8367-8373
DOI: 10.1021/jacs.0c01879


The structure and function of DNA G-Quadruplexes

J Spiegel, S Adhikari and S Balasubramanian
Trends in Chemistry, 2020, 2:2, 123-136
DOI: 10.1016/j.trechm.2019.07.002


A Spontaneous Ring‐Opening Reaction Leads to a Repair‐Resistant Thymine Oxidation Product in Genomic DNA

A Sahakyan, A Mahtey, F Kawasaki and S Balasubramanian
Chem. Bio. Chem., 2020, 21, 320-323
DOI: 10.1002/cbic.201900484


An Activatable Cancer-Targeted Hydrogen Peroxide Probe for Photoacoustic and Fluorescence Imaging

J Weber, L Bollepalli, A Belenguer, M Di Antonio, N De Mitri, J Joseph, S Balasubramanian, C Hunter and S Bohndiek
Cancer Res., 2019, 79, 5407
DOI: 10.1158/0008-5472.CAN-19-0691


Unusual Activity of a Chlamydomonas TET/JBP Family Enzyme

L Aravind, S Balasubramanian and A Rao
Biochemistry, 2019, 58, 3627-3629
DOI: 10.1021/acs.biochem.9b00609


Genetic interactions of G-quadruplexes in humans

K Zyner, D Mulhearn, S Adhikari, S Martínez Cuesta, M Di Antonio, N Erard, G Hannon, D Tannahill and S Balasubramanian
eLife, 2019, 8:e46793
DOI: 10.7554/eLife.46793


Sequencing abasic sites in DNA at single-nucleotide resolution

Z Liu, S Martínez Cuesta, P van Delft and S Balasubramanian
Nature Chemistry, 2019, 11, 629-637
DOI: 10.1038/s41557-019-0279-9


A Photo‐responsive Small‐Molecule Approach for the Opto‐epigenetic Modulation of DNA Methylation

H P Nguyen, S Stewart, M N Kukwikila, S F Jones, D Offenbartl-Stiegert, S Mao, S Balasubramanian, S Beck and S Howorka
Angew. Chem. Int. Ed., 2019, 58, 6620-6624
DOI: 10.1002/anie.201901139


METTL1 Promotes let-7 MicroRNA Processing via m7G Methylations

L Pandolfini, I Barbieri, A Bannister, A Hendrick, B Andrews, N Webster, P Murat, P Mach, R Brandi, S Robson, V Migliori, A Alendar, M d’Onofrio, S Balasubramanian and T Kouzarides
Molecular Cell, 2019, 74, 1-13
DOI: 10.1016/j.molcel.2019.03.040


Detection, Structure and Function of Modified DNA Bases

A Hofer, Z Liu, S Balasubramanian
J. Am. Chem. Soc., 2019, 141, 16, 6420-6429
DOI: 10.1021/jacs.9b01915


Whole genome experimental maps of DNA G-quadruplexes in multiple species

G Marsico, V S Chambers, A B Sahakyan, P McCauley, J M Boutell, M Di Antonio, S Balasubramanian
Nucleic Acids Research, 2019, 47:8, 3862-3874
DOI: 10.1093/nar/gkz179


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

A Sengar, J J Vandana, V S Chambers, M Di Antonio, F R Winnerdy, S Balasubramanian, A T Phan
Nucleic Acids Research, 2018, 47:3, 1564–1572
DOI: 10.1093/nar/gky1179


RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs

P Murat, G Marsico, B Herdy, A Ghanbarian, G Portella and S Balasubramanian
Genome Biology, 2018, 9:229
DOI: 10.1186/s13059-018-1602-2


5-Formylcytosine organises nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells

E-A Raiber, G Portella, S Martinez Cuesta, R Hardisty, P Murat, Z Li, M Iurlaro, W Dean, J Spindel, D Beraldi, Z Liu, M Dawson, W Reik and S Balasubramanian
Nature Chemistry, 2018, 10, 1258–1266
DOI: 10.1038/s41557-018-0149-x


DNA G-quadruplex structures mold the DNA methylome

S-Q Mao, A T Ghanbarian, J Spiegel, S Martinez Cuesta, D Beraldi, M Di Antonio, G Marsico, R Hansel-Hertsch, D Tannahill and S Balasubramanian
Nature Structural & Molecular Biology2018, 25, 951–957
DOI: 10.1038/s41594-018-0131-8


Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts

B Herdy, C Mayer, D Varshney, G Marsico, P Murat, C Taylor, C D’Santos, D Tannahill and S Balasubramanian
Nucleic Acids Research2018, 46:21, 11592–11604
DOI: 10.1093/nar/gky861


Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome

C K Kwok, G Marsico, S Balasubramanian
Cold Spring Harb. Prospect. Biol.2018, 10:a032284
DOI: 10.1101/cshperspect.a032284


Sequencing 5‐Hydroxymethyluracil at Single‐Base Resolution

F Kawasaki, S Martinez Cuesta, D Beraldi, A Mahtey, R Hardisty, M Carrington, S Balasubramanian
Angew. Chem. Int. Ed.2018, 57 (31), 9694-9696
DOI: 10.1002/anie.201804046


Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36

M C Chen, R Tippana, N A Demeshkina, P Murat, S Balasubramanian, S Myong and A R Ferré-D’Amaré
Nature2018, 558, 465–469
DOI: 10.1038/s41586-018-0209-9


NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence

A Parry, M Hoare, D Bihary, R Hansel-Hertsch, S Smith, K Tomimatsu, E Mannion, A Smith, P D’Santos, A Russell,  S Balasubramanian, H Kimura, S Samarajiwa and M Narita
Nature Communications2018, 9, 1840
DOI: 10.1038/s41467-018-04283-9


Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing

R Hansel-Hertsch, J Spiegel, G Marsico, D Tannahill and S Balasubramanian
Nature Protocols2018, 13, 551-564
DOI: 10.1038/nprot.2017.150


Targeting Multiple Effector Pathways in Pancreatic Ductal Adenocarcinoma with a G-Quadruplex-Binding Small Molecule

C Marchetti, K G Zyner, S A Ohnmacht, M Robson, S M Haider, J P Morton, G Marsico, T Vo, S Laughlin-Toth, A A Ahmed, G Di Vita, I Pazitna, M Gunaratnam, R J Besser, A C G Andrade, S Diocou, J A Pike, D Tannahill, R B Pedley, T R J Evans, W D Wilson, S Balasubramanian and S Neidle
J. Med. Chem.2018, 61 (6), 2500–2517
DOI: 10.1021/acs.jmedchem.7b01781


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

A Sahakyan, V S Chambers, G Marsico, T Santner, M Di Antonio and S Balasubramanian
Scientific Reports2017, 7, 14535
DOI: 10.1038/s41598-017-14017-4


DNA sequencing at 40: past, present and future

J Shendure, S Balasubramanian, G M Church, W Gilbert, J Rogers, J A Schloss and R H Waterson
Nature2017, 550, 345-353
DOI: 10.1038/nature24286


Therapeutics: Click and discover

G Vassiliou and S Balasubramanian
Nature2017, 548, 162-164
DOI: 10.1038/548162a


Synthesis and multiple incorporations of 2′-O-methyl-5-hydroxymethyl-, 5-hydroxymethyl- and 5-formylcytidine monomers into RNA oligonucleotides

A Tanpure and S Balasubramanian
ChemBioChem2017, 18, 2236 –2241
DOI: 10.1002/cbic.201700492


Mapping and elucidating the function of modified bases in DNA

E-A Raiber, R Hardisty, P van Delft and S Balasubramanian
Nature Review Chemistry2017, 1, 0069
DOI: 10.1038/s41570-017-0069


Local epigenetic reprogramming induced by G-quadruplex ligands

G Guilbaud, P Murat, B Recolin, B Campbell, A Maiter, J E Sale and S Balasubramanian
Nature Chemistry2017, 9, 1110-1117
DOI: 10.1038/nchem.2828


The profile and dynamics of RNA modifications in animals

P Van Delft, A Akay, S M Huber, C Bueschl, K L M Rudolph, T Di Domenico, R Schuhmacher, E A Miska and S Balasubramanian
ChemBioChem2017, 18, 979-984
DOI: 10.1002/cbic.201700093


Base resolution maps reveal the importance of 5-hydroxymethylcytosine in a human glioblastoma

E-A Raiber, D Beraldi, S Martínez Cuesta, G R McInroy, Z Kingsbury, J Becq, T James, M Lopes, K Allinson, S Field, S Humphray, T Santarius, C Watts, D Bentley and S Balasubramanian
npj Genomic Medicine20172:6
DOI: 10.1038/s41525-017-0007-6


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

R Hänsel-Hertsch, M Di Antonio and S Balasubramanian
Nature Reviews Molecular Cell Biology2017, 18, 279–284
DOI: 10.1038/nrm.2017.3


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

H Xu, M Di Antonio, S McKinney, V Mathew, B Ho, N J O’Neil, N Dos Santos, J Silvester, V Wei, J Garcia, F Kabeer, D Lai, P Soriano, J Banáth, D S Chiu, D Yap, D D Le, F B Ye, A Zhang, K Thu, J Soong, S Lin, A Hsin Chin Tsai, T Osako, T Algara, D N Saunders, J Wong, J Xian, M B Bally, J D Brenton, G W Brown, S P Shah, D Cescon, T W Mak, C Caldas, P C Stirling, P Hieter, S Balasubramanian and S Aparicio
Nature Communications20178, 14432


Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming

I Milagre, T M Stubbs, M R King, J Spindel, F Santos, F Krueger, M Bachman, A Segonds-Pichon, S Balasubramanian, S R Andrews, W Dean and W Reik
Cell Reports201718:5, 1079–1089
DOI: 10.1016/j.celrep.2017.01.008


Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania

F Kawasaki, D Beraldi, R E Hardisty, G R McInroy, P van Delft and S Balasubramanian
Genome Biology201718:23
DOI: 10.1186/s13059-017-1150-1


G-quadruplex structures within the 3’-UTR of LINE-1 elements stimulate retrotransposition

A B Sahakyan, P Murat, C Mayer and S Balasubramanian
Nature Str. Mol. Biol.201724, 243–247
DOI: 10.1038/nsmb.336


2′-O-Methyl-5-hydroxymethylcytidine: A Second Oxidative Derivative of 5-Methylcytidine in RNA

S M Huber, P van Delft, A Tanpure, E A Miska and S Balasubramanian
J. Am. Chem. Soc.2017139 (5), 1766–1769
DOI: 10.1021/jacs.6b12180


Single genome retrieval of context-dependent variability in mutation rates for human germline

A B Sahakyan and S Balasubramanian
BMC Genomics201718:81
DOI: 10.1186/s12864-016-3440-5


Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides

F Kawasaki, P Murat, Z Li, T Santner and S Balasubramanian
Chem. Comm.2017, 53, 1389 – 1392
DOI: 10.1039/C6CC08670E


Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms

T A Horea, F von Meyenna, M Ravichandranc, M Bachman, G Ficz, D Oxley, F Santosa, S Balasubramanian, T P Jurkowskic, and W Reik
PNAS, 2016, 113:42, 12202-12207
DOI: 10.1073/pnas.1608679113


Identification of small molecule inhibitors of the Lin28-mediated blockage of pre-let-7g processing

H L Lightfoot, E A Miska and S Balasubramanian
Org. Biomol. Chem., 2016, 14, 10208-10216
DOI: 10.1039/c6ob01945e


G-quadruplex structures mark human regulatory chromatin

R Hänsel-Hertsch, D Beraldi, S V Lensing, G Marsico, K Zyner, A Parry, M Di Antonio, J Pike, H Kimura, M Narita, D Tannahill and S Balasubramanian
Nature Genetics, 2016, 48, 1267-1272
DOI: 10.1038/ng.3662


rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

C K Kwok, G Marsico, A B Sahakyan, V S Chambers and S Balasubramanian
Nature Methods, 2016, 13, 841-844
DOI: 10.1038/nmeth.3965


DSBCapture: in situ capture and sequencing of DNA breaks

S V Lensing, G Marsico, R Hänsel-Hertsch, E Y Lam, D Tannahill and S Balasubramanian
Nature Methods, 2016, 13, 855-857
DOI: 10.1038/nmeth.3960


An Epigenetics-Inspired DNA-Based Data Storage System

C Mayer, G R McInroy, P Murat, P van Delft and S Balasubramanian
Angew. Chem. Int. Ed., 2016, 55:37, 11144-11148
DOI: 10.1002/anie.201605531


In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine

M Iurlaro, G R McInroy, H E Burgess, W Dean, E-A Raiber, M Bachman, D Beraldi, S Balasubramanian and W Reik
Genome Biology, 2016, 17:141
DOI: 10.1186/s13059-016-1001-5


Structural Analysis using SHALiPE to Reveal RNA G-Quadruplex Formation in Human Precursor MicroRNA

C K Kwok, A Sahakyan and S Balasubramanian
Angew. Chem. Int. Ed., 2016, 55, 8958-8961
DOI: 10.1002/anie.201603562


Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments

G R McInroy, D Beraldi, E-A Raiber, K Modrzynska, P van Delft, O Billker and S Balasubramanian
PLoS ONE, 2016, 3: e)152322
DOI: 10.1371/journal.pone.0152322


Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases

A Sahakyan and S Balasubramanian
BMC Genomics, 2016, 17:225
DOI: 10.1186/s12864-016-2582-9


Photoactivation of Mutant Isocitrate Dehydrogenase 2 Reveals Rapid Cancer-Associated Metabolic and Epigenetic Changes

O S Walker, S J Elsas̈ser, M Mahesh, M Bachman, S Balasubramanian and J W Chin
J. Am. Chem. Soc., 2016, 138, 718 – 721
DOI: 10.1021/jacs.5b07627


Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

S Patalano, A Vlasova, C Wyatt, P Ewels, F Camara, P G Ferreira, C L Asher, T P Jurkowski, A Segonds-Pichon, M Bachman, I González-Navarrete, A E Minoche, F Krueger, E Lowy, M Marcet-Houben, J L Rodriguez-Ales, F S Nascimento, S Balasubramanian, T Gabaldon, J E Tarver, S Andrews, H Himmelbauer, W O H Hughes, R Guigó, W Reik, and S Sumner
PNAS, 2016, 112, 13970 – 13975
DOI: 10.1073/pnas.1515937112


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

V S Chambers, G Marsico, J M Boutell, M Di Antonio, G P Smith and S Balasubramanian
Nature Biotechnology, 2015, 33, 877 – 881
DOI: 10.1038/nbt.3295


FOXM1 binds directly to non-consensus sequences in the human genome

D A Sanders, M V Gormally, G Marsico, D Beraldi, D Tannahill and S Balasubramanian
Genome Biology, 2015, 16:130
DOI: 10.1186/s13059-015-0696-z


5-Formylcytosine can be a stable DNA modification in mammals

M Bachman, S Uribe-Lewis, X Yang, H E Burgess, M Iurlaro, W Reik and S Balasubramanian
Nature Chemical Biology, 2015, 11, 555 – 557
DOI: 10.1038/nchembio.1848


Selective Chemical Labeling of Natural T Modifications in DNA

R E Hardisty, F Kawasaki, A B Sahakyan and S Balasubramanian
J. Am. Chem. Soc., 2015, 137, 9270 – 9272
DOI: 10.1021/jacs.5b03730


C K Kwok and S Balasubramanian
Angew. Chem. Int. Ed., 2015, 54, 6751 – 6754
DOI: 10.1002/anie.201500891


G-quadruplex ligands exhibit differential G-tetrad selectivity

D D Le, M Di Antonio, L K M Chan, and S Balasubramanian
Chem. Commun., 2015, 51, 8048 – 8050
DOI: 10.1039/C5CC02252E


Chemical Methods for Decoding Cytosine Modifications in DNA

M J Booth, E-A Raiber, and S Balasubramanian
Chem. Rev., 2015, 115, 2240 – 2254
DOI: 10.1021/cr5002904


Accurate Measurement of 5-Methylcytosine and 5-Hydroxymethylcytosine in Human Cerebellum DNA by Oxidative Bisulfite on an Array (OxBS-Array)

S F Field, D Beraldi, M Bachman, S K Stewart, S Beck, and S Balasubramanian
PloS ONE, 2015, 10:e0118202t
DOI: 10.1371/journal.pone.0118202


Formation and Abundance of 5-Hydroxymethylcytosine in RNA

S M Huber, P van Delft, L Mendil, M Bachman, K Smollett, F Werner, E A Miska and S Balasubramanian
ChemBioChem., 2015, 16, 752 – 755
DOI: 10.1002/cbic.201500013


Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase

M C Chen, P Murat, K Abecassis, A R Ferre-D’Amare and S Balasubramanian
Nucleic Acids Res., 2015, 43, 2223 – 2231
DOI: 10.1093/nar/gkv051


Decoding Genomes

S Balasubramanian
Biochem. Soc. Trans., 2015, 43, 1 – 5
DOI: 10.1042/BST20140254


5-Formylcytosine alters the structure of the DNA double helix

E Raiber, P Murat, D Y Chirgadze, D Beraldi, B F Luisi and S Balasubramanian
Nature Structural & Molecular Biology, 2015, 22, 44 – 49
DOI: 10.1038/nsmb.2936


Dual binding of an antibody and a small molecule increases the stability of the TERRA G-quadruplex

P M Yangyuoru, M Di Antonio, C Ghimire, G Biffi, S Balasubramanian, and H Mao
Angew. Chem. Int. Ed., 2015, 54, 910 – 913
DOI: 10.1002/anie.201408113


oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips

S K Stewart, T J Morris, P Guilhamon, H Bulstrode, M Bachman, S Balasubramanian and S Beck
Methods, 2015, 72, 9 – 15
DOI: 10.1016/j.ymeth.2014.08.009


Solexa Sequencing: Decoding Genomes on a Population Scale

S Balasubramanian
Clin. Chem., 2015, 61, 21 – 24
DOI: 10.1373/clinchem.2014.221747


Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition

M V Gormally, T S Dexheimer, G Marsico, D A Sanders, C Lowe, D Matak-Vinković, S Michael, A Jadhav, G Rai, D J Maloney, A Simeonov and S Balasubramanian
Nature Communications, 2014, 5:5165
DOI: 10.1038/ncomms6165


Targeting DNA G-Quadruplexes with Helical Small Molecules

S Müller, K Laxmi-Reddy, PV Jena, B Baptiste, Z Dong, F Godde, T Ha, R Rodriguez, S Balasubramanian and I Huc
Chembiochem., 2014, 15, 2563 – 2570
DOI: 10.1002/cbic.201402439


Nucleotide contributions to the structural integrity and DNA replication initiation activity of noncoding Y RNA

I Wang, M P Kowalski, A R Langley, R Rodriguez, S Balasubramanian, S T Hsu, and T Krude
Biochemistry, 2014, 53, 5848 – 5863
DOI: 10.1021/bi500470b


5-Hydroxymethylcytosine is a predominantly stable DNA modification

M Bachman, S Uribe-Lewis, X Yang, M Williams, A Murrell and S Balasubramanian
Nature Chemistry, 2014, 6, 1049 – 1055
DOI: 10.1038/nchem.2064


Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells

D Schiavone, G Guilbaud, P Murat, C Papadopoulou, P Sarkies, M Prioleau, S Balasubramanian and J E Sale
The EMBO Journal, 2014, 33, 2507 – 2520
DOI: 10.15252/embj.201488398


Chemical biology on genomic DNA: minimizing PCR bias

G McInroy, E Raiber, and S Balasubramanian
Chem. Commun., 2014, 50, 12047 – 12049
DOI: 10.1039/C4CC05107F


Elevated Levels of G-Quadruplex Formation in Human Stomach and Liver Cancer

G Biffi, D Tannahill, J Miller, W J Howat and S Balasubramanian
PLoS ONE, 2014, 9, e102711
DOI: 10.1371/journal.pone.0102711


Chemical Biology on the Genome

S Balasubramanian
Bioorg. Med. Chem.,2014, 22, 4356 – 4370
DOI: 10.1016/j.bmc.2014.05.016


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

M Di Antonio, K I E McLuckie, and S Balasubramanian
J. Am. Chem. Soc., 2014, 136, 5860 – 5863
DOI: 10.1021/ja5014344


Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

M J Booth, G Marsico, M Bachman, D Beraldi, and S Balasubramanian
Nature Chemistry, 2014, 6, 435 – 440
DOI: 10.1038/nchem.1893


G-quadruplexes regulate Epstein-Barr virus–encoded nuclear antigen 1 mRNA translation

P Murat, J Zhong, L Lekieffre, N P Cowieson, J L Clancy, T Preiss, S Balasubramanian, R Khanna and J Tellam
Nature Chemical Biology, 2014, 10, 358 – 364
DOI: 10.1038/nchembio.1479


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

G Biffi, M Di Antonio, D Tannahill and S Balasubramanian
Nature Chemistry, 2014, 6, 75 – 80
DOI: 10.1038/nchem.1805


Targeting a c-MYC G-quadruplex DNA with a fragment library

H R Nasiri, N Bell, K McLuckie, J Husby, C Abell, S Neidle and S Balasubramanian
Chem. Commun., 2014, 50, 1704 – 1707
DOI: 10.1039/C3CC48390H


Existence and consequences of G-quadruplex structures in DNA

P Murat and S Balasubramanian
Curr. Opin. Genet. Dev., 2014, 25, 22 – 29
DOI: 10.1016/j.gde.2013.10.012


The binding interaction between long non-coding RNA HOTAIR and PRC2 proteins

L Wu, P Murat, D Matak-Vinkovic, A Murrell and S Balasubramanian
Biochemistry, 2013, 52, 9519 – 9527
DOI: 10.1021/bi401085h


Targeting RNA-Protein Interactions within the Human Immunodeficiency Virus Type 1 Lifecycle

N Bell, A L’Hernault, P Murat, J E Richards, A M Lever, and S Balasubramanian
Biochemistry, 2013, 52, 9269 – 9274
DOI: 10.1021/bi401270d


Mechanochemical Properties of Individual Human Telomeric RNA (TERRA) G-Quadruplexes

P Yangyuoru, A Zhang, Z Shi, D Koirala, S Balasubramanian and H Mao
ChemBioChem., 2013, 14, 1931 – 1935.
DOI: 10.1002/cbic.201300350


A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

M Iurlaro, G Ficz, D Oxley, E Raiber, M Bachman, M J Booth, S Andrews, S Balasubramanian and W Reik
Genome Biology, 2013, 14:R119
DOI: 10.1186/gb-2013-14-10-r119


Oxidative Bisulfite sequencing of 5-methylcytosine and 5-hydroxymethlcytosine

M J Booth, T W B Ost, D Beraldi, N Bell, M Branco, W Reik and S Balasubramanian
Nature Protocols, 2013, 8, 1841 – 1851
DOI: 10.1038/nprot.2013.115


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

P Murat, M V Gormally, D Sanders, M Di Antonio and S Balasubramanian
Chem. Commun., 2013, 49, 8453 – 8455
DOI: 10.1039/C3CC44737E


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

K I E McLuckie, M Di Antonio, H Zecchini, J Xian, C Caldas, B F Krippendorff, D Tannahill, C Lowe and S Balasubramanian
J. Am. Chem. Soc., 2013, 135, 9640 – 9643
DOI: 10.1021/ja404868t


G-quadruplex structures are stable and detectable in human genomic DNA

E Yi Ni Lam, D Beraldi, D Tannahill and S Balasubramanian
Nature Communications, 2013, 4, 1796
DOI: 10.1038/ncomms2792


Down-regulation of androgen receptor transcription by promoter G-quadruplex stabilization as a potential alternative treatment for castrate-resistant prostate cancer

T Mitchell, A Ramos-Montoya, M Di Antonio, P Murat, S Ohnmacht, M Micco, S Jurmeister, L Fryer, S Balasubramanian, S Neidle and D E Neal
Biochemistry, 2013, 52, 1429 – 1436
DOI: 10.1021/bi301349c


Genome-wide mapping of FOXM1 binding reveals co binding with estrogen receptor alpha in breast cancer cells

D A Sanders, C S Ross-Innes, D Beraldi, J S Carroll and S Balasubramanian
Genome Biology, 2013, 14:R6
DOI: 10.1186/gb-2013-14-1-r6


Quantitative visualization of DNA G-quadruplex structures in human cells

G Biffi, D Tannahill, J McCafferty and S Balasubramanian
Nature Chemistry, 2013, 5, 182 – 186
DOI: 10.1038/nchem.1548


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

M Nikan, M Di Antonio, K Abecassis, K McLuckie and S Balasubramanian
Angew. Chem. Int. Ed. , 2013, 52, 1428 – 1431
DOI: 10.1002/anie.201207075


An RNA Hairpin to G-Quadruplex Conformational Transition

A Bugaut, P Murat and S Balasubramanian
J. Am. Chem. Soc., 2012, 134, 19953 – 19956
DOI: 10.1021/ja308665g


The Kinetics and Folding Pathways of Intramolecular G-Quadruplex Nucleic Acids

A Zhang and S Balasubramanian
J. Am. Chem. Soc., 2012, 134, 19297 – 19308
DOI: 10.1021/ja309851t


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

M Di Antonio, G Biffi, A Mariani, E-A Raiber, R Rodriguez and S Balasubramanian
Angew. Chem. Int. Ed, 2012, 51, 11073 – 11078
DOI: 10.1002/anie.201206281


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

S Müller, D A Sanders, M Di Antonio, S Matsis, J F Riou, R Rodriguez and S Balasubramanian
Org. Biomol. Chem., 2012, 10, 6537 – 6546
DOI: 10.1039/C2OB25830G


Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

E-A Raiber, D Beraldi, G Ficz, H Burgess, M R Branco, P Murat, D Oxley, M J Booth, W Reik and S Balasubramanian
Genome Biology, 2012, 13:R69
DOI: 10.1186/gb-2012-13-8-r69


An Intramolecular G-Quadruplex Structure Is Required for Binding of Telomeric Repeat-Containing RNA to the Telomeric Protein TRF2

G Biffi, D Tannahill and S Balasubramanian
J. Am. Chem. Soc., 2012, 134, 11974 – 11976
DOI: 10.1021/ja305734x


50-UTR RNA G-quadruplexes: translation regulation and targeting

A Bugaut and S Balasubramanian
Nucleic Acids Res., 2012, 40, 4727 – 4741
DOI: 10.1093/nar/gks068


Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

M J Booth, M R Branco, G Ficz, D Oxley, F Krueger, W Reik and S Balasubramanian
Science, 2012, 336, 934 – 937
DOI: 10.1126/science.1220671


Experimental Approaches to Identify Cellular G-quadruplex Structures and Functions

M Di Antonio, R Rodriguez and S Balasubramanian
Methods, 2012, 57, 84 – 92
DOI: 10.1016/j.ymeth.2012.01.008


Comparative Structural Effects of HIV-1 Gag and Nucleocapsid Proteins in Binding to and Unwinding of the Viral RNA Packaging Signal

N M Bell, J C Kenyon, S Balasubramanian and A M L Lever
Biochemistry, 2012, 51, 3162 – 3169
DOI: 10.1093/nar/gks068


Small-molecule–induced DNA damage identifies alternative DNA structures in human genes

R Rodriguez, K M Miller, J V Forment, C R Bradshaw, M Nikan, S Britton, T Oelschlaegel, B Xhemalce, S Balasubramanian and S P Jackson
Nature Chemical Biology, 2012, 8, 301 – 310
DOI: 10.1038/nchembio.780


FANCJ coordinates two pathways that maintain epigenetic stability at G-quadruplex DNA

P Sarkies, P Murat, L G Phillips, K J Patel, S Balasubramanian and J E Sale
Nucleic Acids Res., 2012, 40, 1485 – 1498
DOI: 10.1093/nar/gkr868


A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro

E-A Raiber, R Kranaster, E Lam, M Nikan and S Balasubramanian
Nucleic Acids Res., 2012, 40, 1499 – 1508
DOI: 10.1093/nar/gkr882


Demonstration of Ligand Decoration, and Ligand-Induced Perturbation, of G-Quadruplexes in a Plasmid Using Atomic Force Microscopy

I Mela, R Kranaster, R M Henderso, S Balasubramanian and J M Edwardson
Biochemistry, 2012, 51, 578 – 585
DOI: 10.1021/bi201600g


Synthesis of Bis-indole Carboxamides as G-Quadruplex Stabilizing and Inducing Ligands

J Dash, R N Das, N Hegde, G D Pantoş, P Shirude and S Balasubramanian
Chem. Eur. J., 2012, 18, 554 – 64
DOI: 10.1002/chem.201102556


Decoding genomes at high speed: implications for science and medicine

S Balasubramanian
Angew. Chem. Int. Ed., 2011, 50, 12406 – 12410
DOI: 10.1002/anie.201106707


A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands

D Koirala, S Dhakal, B Ashbridge, Y Sannohe, R Rodriguez, H Sugiyama, S Balasubramanian and H Mao
Nature Chemistry, 2011, 3, 782 – 787
DOI: 10.1038/nchem.1126


The transcription factor FOXM1 is a cellular target of the natural product thiostrepton

N S Hegde, D A Sanders, R Rodriguez and S Balasubramanian
Nature Chemistry, 2011, 3, 725 – 731
DOI: 10.1038/nchem.1114


A LIN28-Dependent Structural Change in pre-let-7g Directly Inhibits Dicer Processing

H L Lightfoot, A Bugaut, J Armisen, N J Lehrbach, E A Miska and S Balasubramanian
Biochemistry, 2011, 50, 7514 – 7521
DOI: 10.1021/bi200851d


A Sequence-Independent Analysis of the Loop Length Dependence of Intramolecular RNA G-Quadruplex Stability and Topology

A Zhang, A Bugaut and S Balasubramanian
Biochemistry, 2011, 50, 7251 – 7258
DOI: 10.1021/bi200805j


Sequencing nucleic acids: from chemistry to medicine

S Balasubramanian
Chem. Commun., 2011, 47, 7281 – 7286
DOI: 10.1039/c1cc11078k Highlight


Targeting G‐quadruplexes in gene promoters: a novel anticancer strategy?

S Balasubramanian, L H Hurley and S Neidle
Nature Reviews Drug Discovery, 2011, 10, 261 – 275
DOI: 10.1038/nrd3428


Rudimentary G-quadruplex-based telomere capping in Saccharomyces cerevisiae

J S Smith, Q Chen, L A Yatsunyk, J M Nicoludis, M S Garcia, R Kranaster, S Balasubramanian, D Monchaud, M Teulade-Fichou, L Abramowitz, D C Schultz and F B Johnson
Nature Structural & Molecular Biology, 2011, 18, 478 – 485
DOI: 10.1038/nsmb.2033


Synthesis and Binding Studies of Novel Diethynyl-pyridine Amides with Genomic Promoter DNA G-quadruplexes

J Dash, Z A E Waller, G D Pantos and S Balasubramanian
Chem. Eur. J., 2011, 17, 4571 – 4581
DOI: 10.1002/chem.201003157


G-Quadruplex-Binding Benzo[a]phenoxazines Down-Regulate c-KIT Expression in Human Gastric Carcinoma Cells

K I E McLuckie, Z A E Waller, D A Sanders, D Alves, R Rodriguez, J Dash, G J McKenzie, A R Venkitaraman and S Balasubramanian
J. Am. Chem. Soc., 2011, 133, 2658 – 2663
DOI: 10.1021/ja109474c