DNA constraints control structure of attached macromolecules

Jun 28, 2005

A new method for manipulating macromolecules has been developed by researchers at the University of Illinois at Urbana-Champaign. The technique uses double-stranded DNA to direct the behavior of other molecules. In previous DNA nanotechnology efforts, duplex DNA has been used as a static lattice to construct geometrical objects in three dimensions. Instead of manipulating DNA alone into such shapes, the researchers are using DNA to control the folding and resulting structure of RNA. Eventually, they envision building supramolecular machines whose inner workings are governed by twisted strands of DNA.

In a paper that has been accepted for publication in the Journal of the American Chemical Society, and posted on its Web site, Silverman and graduate student Chandrasekhar Miduturu begin with a piece of unfolded RNA. Through specific chemical reactions, they attach two strands of DNA, each resembling one side of a ladder. The two DNA strands spontaneously bind together, then the researchers add magnesium ions to initiate folding of the RNA.

"Folding of the RNA structure competes with formation of the DNA constraint until a chemical balance is reached," Silverman said. "In some cases, the DNA is like a barnacle, just stuck onto the RNA without perturbing its structure. In other cases, the DNA changes the RNA structure. We can predict which situation will occur based on the shape of the RNA and on the attachment points of the DNA constraint."

In cases where the normal RNA shape and the DNA constraint cannot co-exist simultaneously, the balance between competing RNA and DNA structures is controlled by the concentration of magnesium ions, Silverman said.

In work not yet published, the researchers have also shown that the effects of the DNA constraint on the RNA structure can be modulated by external stimuli such as DNA oligonucleotide strands, protein enzymes and chemical reagents.

While Silverman and Miduturu are currently using RNA as a proof of principle for their DNA constraint studies, they also plan to use the new technique to more effectively study the folding process of RNA. Because they can control RNA structure precisely, they could generate and examine biologically relevant folded and misfolded RNAs. They could also hook the DNA constraints to other molecules, including non-biological macromolecules, to control their folding.

Importantly, the process of manipulating macromolecules with DNA constraints can be either reversible or irreversible, depending on which chemical trigger is used. Like a switch, a particular molecular shape could be turned on and off.

"Another key aspect of DNA constraints is their programmability," Silverman said. "By placing two or more constraints on one molecule, we could generate multiple molecular states that would be programmable by DNA sequence. In other efforts, we would like to control macroscopic assembly processes by influencing the shapes of self-assembling molecular components."

Source: University of Illinois at Urbana-Champaign

Explore further: Flower-like magnetic nanoparticles target difficult tumors

add to favorites email to friend print save as pdf

Related Stories

Unlocking the key to immunological memory in bacteria

Mar 02, 2015

A powerful genome editing tool may soon become even more powerful. Researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) have unlocked the key to how bacteria are able to "steal" genetic ...

New nanodevice defeats drug resistance

Mar 02, 2015

Chemotherapy often shrinks tumors at first, but as cancer cells become resistant to drug treatment, tumors can grow back. A new nanodevice developed by MIT researchers can help overcome that by first blocking ...

Epigenetic 'switch' regulates RNA-protein interactions

Feb 25, 2015

Chemical changes - also known as epigenetic modifications - to messenger RNA (mRNA) are thought to play an important role in gene expression, and have recently been found to affect biological processes such as circadian clock ...

New detection technologies for bacterial pathogens

Feb 19, 2015

In FP7 jargon, RAPTADIAG is categorised as a 'small or medium-scale focused research project'. However, the past two years have seen the consortium turn a novel diagnostic test for bacterial meningitis into ...

Recommended for you

From massive supercomputers come tiniest transistors

15 hours ago

A relentless global effort to shrink transistors has made computers continually faster, cheaper and smaller over the last 40 years. This effort has enabled chipmakers to double the number of transistors on ...

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.