慕尼黑技術大學（Technical University of Munich, TUM）的研究團隊開發了一種可用來建構DNA和蛋白質雜交結構的新方法，為細胞生物學和生物技術和醫學領域的應用開闢了新的想法。
Desoxyribonucleic acid, better known by its
abbreviation DNA, carries our genetic information. But to Prof. Hendrik Dietz
and Florian Praetorius from TUM, DNA is also an excellent building material for
nanostructures. Folding DNA to create three-dimensional shapes using a
technique known as "DNA origami" is a long-established method in this
But there are limits to this approach,
explains Dietz. The "construction work" always takes place outside of
biological systems and many components must be chemically synthesized.
"Creating user-defined structures in sizes on the order of 10 to 100
nanometers inside a cell remains a great challenge," he adds. Their newly
developed technique now allows the researchers to use proteins to fold
double-stranded DNA into desired three-dimensional shapes. Here, both the DNA
and the required proteins can be genetically encoded and produced inside cells.
act as staples
Designed "staple proteins" based
on TAL effectors are the key to the method. TAL effectors are produced in
nature by certain bacteria that infect plants and are able to bind to specific
sequences in the plant DNA, thereby neutralizing the plant's defense
mechanisms. "We've constructed variants of the TAL proteins which
simultaneously recognize two custom target sequences at different sites in the
DNA and then basically staple them together," says Dietz. "This was
exactly the property we needed: proteins that can staple DNA together."
The second component of the system is a DNA
double strand containing multiple binding sequences that can be recognized and
linked by a set of different staple proteins. "In the simplest case a loop
can be created by binding two points to one another," Praetorius explains.
"When several of these binding sites exist in the DNA, it's possible to
build more complex shapes." An essential aspect of the researcher's work
was therefore determining a set of rules for arranging the staple proteins
themselves and how to distribute the binding sequences on the DNA double strand
in order to create the desired form.
tools for fundamental research
What's more, the staple proteins serve as
anchor points for additional proteins: A method referred to as genetic fusion
can be used to attach any functional protein domain desired. The hybrid
structures made of DNA and proteins then function as a three-dimensional
framework which can put the other protein domains into a particular spatial
position. All the building blocks for the DNA protein hybrid structures can be
produced by the cell itself and then assemble themselves autonomously. The
researchers were able to produce the hybrids in environments resembling cells
starting from genetic information. "There is a fairly high probability
that this will also work in actual cells," says Dietz.
The new method paves the way for
controlling the spatial arrangement of molecules in living systems, which
allows probing fundamental processes. For example, it's assumed that the
spatial arrangement of the genome has a substantial influence on which genes
can be read and how efficient the reading process is. The intentional creation
of loops using TAL-DNA hybrid structures in genomic DNA may provide a tool for
investigating such processes.
It would also be possible to geometrically
position a series of proteins inside and outside the cell in custom ways in
order to investigate the influence of spatial proximity for example on
information processing in the cell. The spatial proximity of certain enzymes
could also make processes in biotechnology more efficient. Lastly, it would
also be conceivable to utilize protein-DNA hybrid structures for example to
better stimulate the immune response of cells, which can depend on the precise
geometrical arrangement of multiple antigens.
University of Munich. " Designer
proteins fold DNA: Biophysicists construct complex hybrid structures using DNA
and proteins. " ScienceDaily, 23 March, 2017.
Praetorius and H. Dietz. Self-assembly of genetically encoded DNA-protein
hybrid nanoscale shapes. Science, 2017. DOI: 10.1126/science.aaf5488