Research

DNA MODIFICATION AND DNA SENSING

In this area of research, we study modified DNA strands containing photo-active or redox-active groups that give DNA extra functionality. Different topics are outlined below:

DNA Base Sensing: We design modified DNA probes that can detect variations at single nucleobase sites in sequences of target DNA. These base variations, which are termed single nucleotide polymorphisms (SNPs) and occur naturally in the human genome, are important for our understanding of the origin of diseases that have a genetic component. In our approach to SNP detection via fluorescence sensing, we make a probe strand of modified DNA containing an anthracene tag. The sensing process operates through the tag emission intensity being affected by the identity and location of the base in the target strand upon duplex formation (hybridisation). Sensing takes place either via a so-called base-adjacent strategy [1,2] (through base-pair mismatching) or a base-opposite strategy.[3] The latter approach is shown in the scheme below, where B = A, C, G or T. Base changes associated with mutations linked to cancer can also be detected in this manner.

anthdna

As well as base changes, this methodology can be used to detect base modifications at single sites, for example cytosine versus 5-methylcytosine. The graph below shows that anthracene fluorescence from a probe can either increase or decrease depending on the methylation status of a cytosine base within a sequence of target DNA. Methylation is an important epigenetic process that controls gene expression, with both hyper- and hypo-methylation linked to cancer development.[4]

methylspec

Recently we have reported a new approach to SNP sensing that uses electrochemistry rather than fluorescence, by attaching redox-active Cu(II)-containing cyclidene macrocycles to DNA probe strands.[5]

Much of our anthracene-based DNA work is carried out in collaboration with the groups of Joe Vyle in Belfast and Dario Bassani in Bordeaux and involves photochromic systems as well as sensing systems. Molecular modelling calculations are carried out in partnership with John Wilkie here in Birmingham.

Relevant publications:

[1]N.Moran,D.M.Bassani,J.P.Desvergne,S.Keiper,P.A.S.Lowden,J.S.Vyle,J.H.R.Tucker, Chem.Commun.,2006,5003.

[2]J.L.H.A.Duprey,D.M.Bassani,E.I.Hyde,C.Ludwig,A.Rodger,J.S.Vyle,J.Wilkie,Z.Y.Zhao,J.H.R.Tucker, Supramol. Chem.,2011,23,273.

[3]J.L.H.A.Duprey,Z.Y.Zhao,D.M.Bassani,J.Manchester,J.S.Vyle,J.H.R.Tucker, Chem. Commun.,2011,47,6629.

[4]J.L.H.A.Duprey,G.A.Bullen,Z.Y.Zhao,D.M.Bassani, A.F.A.Peacock,J.Wilkie,J.H.R.Tucker, ACS Chem. Biol., 2016, 11, 717.

[5]J.L.H.A.Duprey, J.Carr-Smith,S.L.Horswell,J.Kowalski,J.H.R. Tucker, J. Am. Chem. Soc., 2016, 138, 746.

Ferrocene Nucleic Acids (FcNA):  Many chemists are interested in establishing whether unnatural/synthetic versions of nucleic acids (often called xeno nucleic acids or XNAs) can mimic the properties and function of natural versions (i.e. DNA or RNA). Our research focuses on the development of a metal-based analogues of DNA and in particular one that we call FcNA (see below), where the repeating sugar-phosphate-sugar unit in DNA is replaced with a ferrocene (Cp-Fe-Cp) unit. We envisage that the redox properties of these metal-containing oligos could be useful for probing a range of biologically-relevant analytes and metals. So far we have fully synthesised some monomeric components[6] as well as a ferrocene nucleic acid (FcNA) oligomer using automated DNA synthesis, which displays quasi-reversible redox behaviour.[7]

ferrocenecover.png

Relevant publications:

[6]H.V.Nguyen,A.Sallusatrau,L.Male,P.J.Thornton,J.H.R.Tucker, Organometallics,2011,30,5284

[7]H.V.Nguyen,Z.-Y.Zhao,A.Sallustrau,S.L.Horswell,L.Male,A.Mulas, J.H.R.Tucker, Chem.Commun.,2012, 48, 12165.

ELECTROCHEMICAL CHIRAL SENSORS  

Electrochemical supramolecular sensing is an established field and many examples of sensors for various charged and neutral species are known. However supramolecular approaches to chiral electrochemical sensors are rare. Our work consists of observing differences in the redox properties of complexes between opposite enantiomers of various guests and enantiopure ferrocene-based receptors. The binding interaction is mediated either by the formation of hydrogen bonds using urea-based receptors [8] or, as shown below, the formation of boronate ester complexes through reactions with chiral diols.[9] This latter approach has allowed us to demonstrate the principle of enantiomeric excess determination using electrochemistry. The two diastereomeric complexes formed between (R) and (S)-Binol with the (R)-boronic acid receptor give significantly different ferrocene-centred electrode potentials as shown below, demonstrating effective electrochemical chiral sensing. This difference in redox response can be used to quantify high levels of enantiomeric excess in mixtures of Binol enantiomers.

electrochemshift.png

We are also interested in developing homochiral redox-active monolayers. In collaboration with Chris Moody at Nottingham and Sarah Horswell at Birmingham, we have reported a new achiral tether for this purpose, isolipoic acid.[10]

Relevant publications:


[8]A.Mulas, Y.Willener, J. Carr-Smith, K.M. Joly, L Male, C.J. Moody, S.L. Horswell, H.V. Nguyen, J.H.R. Tucker, Dalton Trans, 2015, 44, 7268.

[9]G.Mirri,S.D.Bull,P.N.Horton,T.D.James,L.Male,J.H.R.Tucker,J.Am.Chem.Soc.,2010,132,8903.

[10]K.M.Joly,G.Mirri,Y.Willener,S.L.Horswell,C.J.Moody,J.H.R.Tucker,J.Org.Chem.,2010,75,2395.

MOLECULAR MOTION 

Over the past few years, we have studied molecular motion in the form of nitrogen inversion in aziridines, in collaboration with Mike Shipman and colleagues at Warwick. The strained structure in the three-membered aziridine ring means that the rate of nitrogen inversion, which occurs in all amines, is slow enough to be monitored by variable temperature NMR spectroscopy. We have shown how this inversion can be controlled by various external inputs such as a redox process[11] and metal complexation.[12] In the example shown below, inversion is faster for the ortho-substituted pyridine due to the formation of a single intramolecular H-bond, which is formed in the transition state between the pyridine nitrogen and an amide hydrogen.[13]

aziriswitch.png

Recently we have been looking at molecular motion (shuttling) in H-bonded interlocked structures in collaboration with the McClenaghan group in Bordeaux.

Relevant publications:

[11]M.W.Davies,M.Shipman,J.H.R.Tucker,T.R.Walsh,J.Am.Chem.Soc.,2006,128,14260.

[12]M.W.Davies,A.J.Clarke,G.J.Clarkson,M.Shipman,J.H.R.Tucker,Chem.Commun.,2007,5078.

[13]L.Giordano,C.T.Hoang,M.Shipman,J.H.R.Tucker,T.R.Walsh,Angew.Chem.Int.Ed.,2011,50,741.

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