Chemical Science Blog

A new, fast way to analyse DNA has been developed by European scientists that could be used to sequence the genomes of viruses and in the future help tackle genetic disorders such as schizophrenia and congenital heart defects. 

Current DNA sequencing methods are able to sequence short regions of the genome (30² to 1500² bases in length). Regions that are either duplicated or deleted relative to a reference genome are an important cause of structural variation in the human genome with links to a variety of genetic disorders. Using current sequencing methods, studying these repeats is time consuming and labour intensive. 

Now, Robert Neely and colleagues, at Catholic University Leuven, Belgium, have used a DNA methyltransferase enzyme to label the 5′-GCGC-3′ DNA sequences with a fluorescent marker. Immobilising and stretching the DNA on a surface then produces a unique and reproducible pattern when combined with the fluorescent markers. The result is a ‘fluorocode’ – a simple description of the DNA sequence, which can be read and analyzed like a barcode. 

Sequences of DNA are tagged with a fluorescent marker

DNA barcodes using fluorescent tagging can be read quickly as labelled samples pass a detector, but Neely’s fluorocode gives significantly enhanced resolution and uses a much smaller number of DNA molecules. ‘The method from unlabelled DNA to fluorocode can be achieved in less than 8 hours for a DNA molecule that is around 50000 bases in length,’ says Neely. Current single molecule mapping methods have a timeframe of around one week for analysing individual genomes. 

Kalim Mir, an expert in DNA sequencing and genomics at the Wellcome Trust Centre for Human Genetics, University of Oxford, comments, ‘the advantage the system has over conventional optical mapping is that it can provide ultra-high density mapping of genomic DNA and could easily be extended to much longer fragments from larger genomes, from bacteria to humans. The most significant challenge the authors face is to scale the technique up to the human genome.’ 

The group now plan to scale the fluorocode up from viral genomes to bacterial and on to eukaryotic genomes with the immediate aim of producing multi-coloured fluorocodes with even more detail. 

Carl Saxton

Find out more in the Chemical Science Edge article.

Carbon nanotubes can now be functionalised on a large scale more cleanly and efficiently than before, improving their commercial viability for engineering, catalysis and bionanotechnology.

Milo Shaffer, at Imperial College London, and colleagues, have exploited existing surface oxide defects present in most carbon nanotubes to attach a variety of organic molecules to their surfaces. Surface functionalisation can improve a nanotube’s compatibility with particular environments, such as electrolytes, or can provide a direct function, such as catalytic activity. Conventional functionalisation methods are time-consuming and inconvenient. They also generate a lot of liquid waste, commonly toxic or corrosive. Although some solvent-free methods are known, they are poorly reproducible and often degrade the graphite framework and affect the nanotube’s intrinsic properties.

Shaffer heated the nanotubes to 1000 ºC under an inert atmosphere, which caused the defect groups to desorb, leaving reactive surface radicals. When he added functional monomers, such as vinyl compounds, to the activated nanotubes, the monomers polymerised, forming oligomers grafted to the nanotube surface.

This thermochemical method can be applied entirely in the gas phase, which simplifies work-up, improves scalability and makes it compatible with existing gas phase processes for commercially producing nanotubes.

Read the full Chemical Science Edge Article to find out more.

Gene therapy has the potential to revolutionise personal medicine but delivering the genes into cells is a major challenge. Dendrons offer a potential solution as their many ligands bind strongly to DNA but now scientists are reporting that smaller dendrons with fewer ligands can actually be better at gene delivery than larger ones. 

Previous studies show that larger dendrons bind DNA more strongly than smaller ones because they have a higher positive charge and form more contacts with the DNA. But as large dendrons are more difficult to synthesise, David Smith, at the University of York, UK, and colleagues have been investigating other ways to improve dendron–DNA interactions.

The team designed spermine-functionalised dendrons capable of self-assembling then used multiscale modelling to understand the impact of the self-assembly process on their ability to bind and deliver DNA. Surprisingly, the smaller dendrons were better at binding DNA because they self-assembled more effectively to form an aggregate with a higher charge density. Also, two hydrophobic cholesterol units (rather than one) at the dendron focal point resulted in enhanced gene delivery in vitro. These dendrons assemble into a different shape and pack DNA more effectively, says Smith.

To find out more, read the Edge article.

Scientists report the first example of Brønsted acid asymmetric catalysis in aqueous solution.

Water is an attractive reaction medium as it is cheap, clean, non-toxic and non-flammable. Also, its high heat capacity makes it ideally suited to exothermic reactions on an industrial scale. There are a number of reports of metal catalysed asymmetric reactions in the presence of water, as well as organocatalytic reactions involving covalent bonding, but until now a non-covalent, asymmetric organocatalytic reaction has remained elusive.

Magnus Rueping and Thomas Theissmann at Aachen University, Germany, performed enantioselective hydrogenation of quinolines using a chiral phosphoric acid catalyst in water. Phosphoric acid forms a hydrogen bond with the quinoline, and directs the dihydropridine hydride donor to a particular face.

This hydrogen-bonding catalysis occurs despite the fact that water is an excellent hydrogen donor, due to the phenomenon of ‘hydrophobic hydration’. Interaction between water molecules at the hydrophobic-hydrophilic interface causes the contact surface between water and substrate molecules to be minimised, reducing the possibility for water to participate in hydrogen-bonding, explains Rueping. The selectivity of the catalyst was further improved by adding bulky organic side chains that create a hydrophobic pocket for the substrate.

A hydrophobic site is created allowing catalysis to take place

Rueping says, ‘Non covalent asymmetric activation in aqueous solution has been considered impossible due to fast proton transfer in protic media. Our solution based on the principle of hydrophobic interaction allowed us to develop a Brønsted acid catalysed reaction in aqueous solution that provides the products in good yields and with excellent enantioselectivities.’

Peter Dalko from the Paris Descartes University in France says, ‘the discovery of the efficient reaction conditions is only part of the cake, since the rational behind the observed selectivity is also worth reflection. Hydrophobic interactions are well known in enzymology and are evoked to explain stereoselectivity in many enzymatic transformations. This concept is now emerging in chemistry as a major paradigm.’

Rueping is confident that it could be carried out on a larger scale. ‘Typically we use one equivalent of the dihydropyridine, but for large scale processes catalytic amounts of hydride donor would be used. Given that recycling of dihydroypyridines in water is already possible, the new Brønsted acid catalysed process in aqueous solution paves the way for large scale application.’

Jacob Bush

Read the full Chemical Science Edge article

Only a single metal centre is needed to catalyse the reduction of oxygen to produce water, opening the door to more efficient fuel cells in the future, say researchers in the US.

Converting solar energy to chemical energy using solar fuel cells and releasing stored energy from hydrogen fuel cells involves two key multielectron redox reactions – oxidising water to evolve oxygen and the reverse, reducing oxygen to water. It is the second reaction that limits the application of hydrogen fuel cells at the moment, as it generally requires expensive metal catalysts, such as platinum.

Cobalt porphyrin catalyst could improve fuel cell technology

Nature achieves similar results in many different catalytic systems using metalloenzymes that contain bi- or multimetallic reaction sites, which has provided inspiration for development of bimetallic porphyrin catalysts. Now Daniel Nocera and colleagues at Massachusetts Institute of Technology have shown for the first time that single centre cobalt porphyrins anchored on carbon nanotubes can efficiently catalyse the reduction of oxygen, as long as they also contain a proton transfer group.

The positioning of the proton transfer group – in this case a carboxylic acid – the correct distance away from the cobalt is essential to stops the catalyst from partially reducing the oxygen, which is often a key problem in maintaining the efficiency of these reactions, explains Nocera.

Nocera’s porphyrins are much more efficient than existing cobalt catalysts and are made easily in two steps, so could invigorate the design of future fuel cells using cobalt over its more costly metal cousins.

Minhua Shao, an expert in fuel cell technologies at UTC Power in the US, believes that the results are ‘important to guide the design and development of non-precious metal electrocatalysts for oxygen reduction reaction in fuel cells’.

This is something Nocera is keen to develop, saying that he is now ‘focusing on improving the catalysts by lowering the amount of energy needed for the reaction’.