Threaded through a pore: Single-molecule detection of hydroxymethylcytosine in DNA

April 25, 2013
Threaded through a pore
Credit: Angewandte Chemie

(Phys.org) —Changes in the bases that make up DNA act as markers, telling a cell which genes it should read and which it shouldn't. In the journal Angewandte Chemie, a British team has now introduced a new method that makes it possible to enrich the rare gene segments that contain the modified base hydroxymethylcytosine and to identify individual hydroxymethylcytosine molecules in DNA. Such modifications are associated with autoimmune diseases and cancer.

The bases adenine, guanine, cytosine, and thymine make up the genetic code. Every cell of the body contains an identical set of complete genetic material. However, the various tissues in the body are very different from each other. This is because the cells have the ability to transcribe only a specific selection of genes into proteins, leaving other genes unused. Epigenetic factors such as "markers" on the DNA control this process. The base cytosine can be equipped with different side groups, such as a methyl or hydroxymethyl group. Dense methylation of regulatory switches off the corresponding genes. During development of the embryo, methylation patterns initiate . Changes in the methylation patterns are associated with and cancer. Hydroxymethylcytosine patterns also seem to play a role in the differentiation of as well as in gene expression in cells of the .

Sequencing techniques that can be used to specifically detect epigenetic bases are thus very important. To date, the identification of hydroxymethylcytosine has required complex, expensive, or error-prone processes. A team led by Hagan Bayley at the University of Oxford University has now developed a chemical modification that allows for the differentiation of hydroxymethylcytosine and methylcytosine through sequencing in nanopores.

Developed by Oxford , a company formed by Hagan Bayley in 2005, the nanopore method is a highly promising alternative to the sequencing of individual DNA molecules without an amplification step. Fed by an enzyme, a single strand of DNA threads through a membrane-embedded protein pore. Depending on which of the bases is in the narrowest part of the pore at a given time, there is a characteristic change in the flow of current through the pore.

A chemical reaction between hydroxymethylcytosine, bisulfite, and a cysteine-containing peptide that leaves the other bases—including methylcytosine—unchanged, greatly improves the resolution as the various bases result in differences in current.

Importantly, it is possible to attach a fluorescent marker to the modified site, or a molecular "eye" that can be used to attach the rare hydroxymethylcytosine-containing DNA fragments to "hooks" that allow the fragments to be enriched over unmodified fragments, enabling rapid sequence analysis.

Explore further: New nucleotide could revolutionize epigenetics

More information: Bayley, H. Single-Molecule Detection of 5-Hydroxymethylcytosine in DNA through Chemical Modification and Nanopore Analysis, Angewandte Chemie International Edition. Permalink to the article: dx.doi.org/10.1002/anie.201300413

Related Stories

New nucleotide could revolutionize epigenetics

April 16, 2009

Anyone who studied a little genetics in high school has heard of adenine, thymine, guanine and cytosine - the A,T,G and C that make up the DNA code. But those are not the whole story. The rise of epigenetics in the past decade ...

Scientists identify seventh and eighth bases of DNA

July 21, 2011

For decades, scientists have known that DNA consists of four basic units -- adenine, guanine, thymine and cytosine. Those four bases have been taught in science textbooks and have formed the basis of the growing knowledge ...

Decoding DNA's annotations

January 20, 2012

In the currently hot research area known as ‘epigenetics’, researchers are discovering that offspring inherit much more from their parents than just their genes. Individuals also inherit detailed instructions on ...

Recommended for you

Findings illuminate animal evolution in protein function

July 27, 2015

Virginia Commonwealth University and University of Richmond researchers recently teamed up to explore the inner workings of cells and shed light on the 400–600 million years of evolution between humans and early animals ...

New polymer able to store energy at higher temperatures

July 30, 2015

(Phys.org)—A team of researchers at the Pennsylvania State University has created a new polymer that is able to store energy at higher temperatures than conventional polymers without breaking down. In their paper published ...

How to look for a few good catalysts

July 30, 2015

Two key physical phenomena take place at the surfaces of materials: catalysis and wetting. A catalyst enhances the rate of chemical reactions; wetting refers to how liquids spread across a surface.

Yarn from slaughterhouse waste

July 29, 2015

ETH researchers have developed a yarn from ordinary gelatine that has good qualities similar to those of merino wool fibers. Now they are working on making the yarn even more water resistant.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.