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Instruments / Technical Area	Publication Details	Published
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-Macromolecular Crystallography	5-Formylcytosine does not change the global structure of DNA Jack S. Hardwick , Denis Ptchelkine , Afaf H. El-Sagheer , Ian Tear , Daniel Singleton , Simon E. V. Phillips , Andrew N. Lane , Tom Brown Nature Structural & Molecular Biology 74 DOI: 10.1038/nsmb.3411 Show Abstract ▼ Abstract: The mechanism by which the recently identified DNA modification 5-formylcytosine (fC) is recognized by epigenetic writer and reader proteins is not known. Recently, an unusual DNA structure, F-DNA, has been proposed as the basis for enzyme recognition of clusters of fC. We used NMR and X-ray crystallography to compare several modified DNA duplexes with unmodified analogs and found that in the crystal state the duplexes all belong to the A family, whereas in solution they are all members of the B family. We found that, contrary to previous findings, fC does not significantly affect the structure of DNA, although there are modest local differences at the modification sites. Hence, global conformation changes are unlikely to account for the recognition of this modified base, and our structural data favor a mechanism that operates at base-pair resolution for the recognition of fC by epigenome-modifying enzymes.	May 2017
B23-Circular Dichroism	Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling Daniel Singleton , Rohanah Hussain , Giuliano Siligardi , Pawan Kumar , Patrick J. Hrdlicka , Nina Berova , Eugen Stulz Organic & Biomolecular Chemistry DOI: 10.1039/C5OB01681A Diamond Proposal Number(s): [5872, 6703, 6705] Open Access Show Abstract ▼ Abstract: Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargylamide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.	Sep 2015
B23-Circular Dichroism	Porphyrin substituted DNA: building blocks for novel nanostructures Daniel Singleton Diamond Proposal Number(s): [5872, 6703] Show Abstract ▼ Abstract: Porphyrin-modified DNA duplexes have been studied in detail for the last 10 years. It is well known that G-rich DNA sequences of the type (GGGX)4 can form stable intramolecular quadruplex structures containing stacks of G quartets in the presence of monovalent cations such as potassium. The synthesis of novel G-quadruplex forming DNA sequences based on the human telomeric repeat (GGGTTA)x where porphyrins are covalently attached to thymidine is presented. It is shown that the porphyrin modification offers a large degree of stabilisation to the G-quadruplex. Structural studies have revealed that the porphyrin modification does not bias the formation of a single G quadruplex. However, one exception was observed for a G quadruplex with two porphyrin modifications. Further insight into the interactions between the porphyrin and the G-quadruplex were achieved by molecular dynamic simulations. The synthesis of novel porphyrin-modified locked nucleic acids (LNA) is presented. It was hoped that the LNA modification would provide stability to the porphyrin-modified DNA duplex as porphyrin modifications have previously been found to destabilise duplex DNA. The structure and stability of the DNA was assessed in detail using circular dichroism spectroscopy. Finally, a new method of synthesising porphyrin-modified DNA using polymerases to incorporate porphyrin triphosphates into oligonucleotides is presented. The synthesis of novel porphyrin triphosphates is described. A variety of polymerases were assessed on whether they could incorporate these triphosphates into oligonucleotides. Multiple incorporations of these porphyrin-modified triphosphates showed that they were a good substrate for certain polymerases and with further development this method could be a viable route to synthesis of porphyrin-modified DNA.	Oct 2012
B23-Circular Dichroism	Synthesis of DNA-Porphyrin Arrays Daniel Singleton , Tom Bandy , Imenne Bouamaied , Ashley Brewer , Jon Burns , Simon Gerrard , Gabriella Marth , Thao Nguyen , Guiliano Siligardi , Eugen Stulz Sixth International Conference on Porphyrins and Phthalocyanines (ICPP-6),	Jul 2010
B23-Circular Dichroism	G-Quadruplexes with Covalently Bound Porphyrins Daniel Singleton , Keith Fox , Guiliano Siligardi , Eugen Stulz Sixth International Conference on Porphyrins and Phthalocyanines (ICPP-6),	Jul 2010

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