Researchers Initiate a New Method Based on Hoogsteen Interactions for Organizing Double-Stranded DNA


A human cell contains approximately 2 meters of DNA, which includes the essential genetic information of an individual. If one were to untangle and stretch out all the DNA contained in one person, it would be a great distance – enough to reach the sun and back 60 times back. To control the astounding volume of biological information, cells condense their DNA into tightly packed chromosomes.

“Think of DNA as a piece of paper on which all of our genetic information is written.” Said Minke AD Nijenhuis, the author’s correspondent. “Paper is folded into a very tight structure to fit all of that information into the nucleus of a small cell. However, to read the information, parts of the paper have to be unfolded and then folded back. This spatial organization of our genetic code is the main mechanism of life. Therefore we wanted to create a methodology that would enable researchers to engineer and study condensation of double-stranded DNA.”

The three helix structure provides protection and compactness

Natural DNA is often double-stranded: one strand for encoding genes and one spare strand, intertwined in a double helix. The double helix is ​​stabilized by the Watson-Crick interaction, which allows the two strands to recognize and pair with each other. However there is another, less well-known class of interactions between DNA. This so-called normal or reverse Hoogsteen interaction allows the third strand to join, forming a beautiful triple helix (Figure 2).

In a recent paper, published in Advanced Materials, researchers from Gothelf’s lab started a general method for organizing double-stranded DNA, based on Hoogsteen interactions. This study clearly shows that the triplex-forming strands are capable of sharply bending or “folding” double-stranded DNA to create a compact structure. The appearance of these structures ranges from hollow two-dimensional shapes to solid 3D constructions and everything in between, including structures that resemble potted flowers. Gothelf and co-workers named their method triplex origami (Figure 3).

With triplex origami, scientists can achieve a previously unimaginable level of artificial control over the shape of double-stranded DNA, opening new avenues for exploration. It has recently been suggested that triplex formation plays a role in the natural compaction of genetic DNA and current research may offer insight into this fundamental biological process.

Potential in gene therapy and beyond

This work also shows that Hoogsteen-mediated triplex formation protects DNA from enzymatic degradation. Therefore, the ability to condense and protect DNA by the triplex origami method may have major implications for gene therapy, in which diseased cells are repaired by encoding lost function into transportable parts of double-stranded DNA.

This biological wonder of DNA sequences and structures has also been applied in nanoscale materials engineering, yielding applications in therapeutics, diagnostics and many other fields. “Over the past four decades, DNA nanotechnology has relied almost exclusively on basic Watson-Crick interactions to pair single DNA strands and organize them into specialized nanostructures.” Says Professor Kurt V. Gothelf. “We now know that the Hoogsteen interaction has the same potential to regulate double-stranded DNA, which presents a significant conceptual extension to this field.”

Gothelf and co-workers demonstrated that Hoogsteen-mediated folding is compatible with state-of-the-art Watson-Crick-based methods. Because of the comparative rigidity of double-stranded DNA, however, triplex origami structures require less starting material. This allows larger structures to be formed at a much lower cost.

This new method has the limitation that forming triplexes usually requires long stretches of purine bases in double-stranded DNA and therefore the researchers used artificial DNA sequences, not natural genetic DNA. However, in the future they will work to overcome these limitations.



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