NUS researchers identify a novel double-stranded DNA structure

Aug 03, 2012
This novel double-stranded DNA structure produced through mechanical stretching has been successfully demonstrated by researchers from the National University of Singapore. Credit: National University of Singapore

By way of mechanical stretching, National University of Singapore researchers identify a novel double-stranded DNA structure, thus successfully resolving a 16-year-old scientific debate over the existence of a double-stranded DNA structure.

Double-stranded DNA has often been described as a right-handed helical structure, known as B-DNA. To perform its multiple functions, double-stranded DNA has multiple structures depending on conditions. For example, the melted DNA bubble forms during and the left-handed helical Z-DNA forms hypothetically during transcriptional regulations.

Scientists have been proposing a novel form of double-stranded DNA structure since 1996. Referred to as 'S-DNA', it is produced from stretching the B-form DNA beyond a certain 'transition force' of around 65 pN to approximately 1.7-fold in length (termed as DNA overstretching transition). Its existence has sparked a 16-year scientific debate since it was proposed, as many other evidences suggested that DNA overstretching transition was merely a force-induced DNA melting transition, leading to peeled-apart single-stranded DNA.

At National University of Singapore (NUS), the research was led by Associate Professor Jie Yan, from the Department of Physics, Faculty of Science and Mechanobiology Institute, Singapore. It succeeded in demonstrating the intricacies of the DNA mechanics in highly sensitive single-DNA stretching experiments.

Assoc Prof Yan and his team found that DNA overstretching may involve two transitions that are distinct in their transition kinetics, namely, a slower hysteretic peeling transition to peeled-apart single-stranded DNA and a faster non-hysteretic transition to an unknown DNA structure. However, whether the unknown produced from the non-hysteretic transition is the S-DNA or two single-stranded through inside-DNA-melting, remains a question.

Their findings were published in .

In another recent work published in Proceedings of the National Academy of Sciences, Assoc Prof Yan and co-researchers examined the thermodynamics associated with the two transitions. They found that the non-hysteretic transition was associated with a small negative entropy change, in contrast to the large positive entropy change found during the hysteretic peeling transition. This result strongly favors DNA re-arrangement into a highly ordered, non-melted state during the non-hyteretic transition. They also demonstrated that the selection between the two transitions was dependent on DNA base-pair stability and could be represented in a multi-dimensional phase diagram.

Their results not only brought clarity to the scientific debate of whether S-DNA exists, but also provided important insights to the possible structures and functions of the mysterious S-DNA.

Given its elongated , the S-DNA may be a potential binding substrate for DNA intercalators, including those used in chemotherapeutic treatment to inhibit DNA replication in rapidly growing cancer cells. In cells, many DNA-binding proteins utilize side chain intercalation to distort the DNA backbone. Therefore, the S-DNA may also be a potential binding substrate for these proteins that occur in living organisms.

Explore further: Evolution: The genetic connivances of digits and genitals

add to favorites email to friend print save as pdf

Related Stories

Elusive Z- DNA found on nucleosomes

Jan 20, 2012

New research published in BioMed Central's open access journal Cell & Bioscience is the first to show that left-handed Z-DNA, normally only found at sites where DNA is being copied, can also form on nucleosomes.

DNA falls apart when you pull it

May 20, 2011

DNA falls apart when you pull it with a tiny force: the two strands that constitute a DNA molecule disconnect. Peter Gross of VU University Amsterdam has shown this in his PhD research project. With this research, ...

Unraveling the DNA stretching mystery

Jan 20, 2011

(PhysOrg.com) -- Using a new experimental test structure, biophysicists at JILA have unraveled part of a 15-year mystery in the mechanics of DNA -- just how the molecule manages to suddenly extend to almost ...

Common mechanisms for viral DNA replication

Jan 23, 2007

How DNA replicates is a critical question for understanding life. DNA replication remains difficult to investigate in eukaryotes,where it occurs within the confines of the double-membrane nucleus.

Recommended for you

Evolution: The genetic connivances of digits and genitals

8 hours ago

During the development of mammals, the growth and organization of digits are orchestrated by Hox genes, which are activated very early in precise regions of the embryo. These "architect genes" are themselves regulated by ...

Surrogate sushi: Japan biotech for bluefin tuna

18 hours ago

Of all the overfished fish in the seas, luscious, fatty bluefin tuna are among the most threatened. Marine scientist Goro Yamazaki, who is known in this seaside community as "Young Mr. Fish," is working to ...

Scientists map mouse genome's 'mission control centers'

Nov 19, 2014

When the mouse and human genomes were catalogued more than 10 years ago, an international team of researchers set out to understand and compare the "mission control centers" found throughout the large stretches ...

User comments : 0

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.