Nav: Home

Prebiotic evolution: Hairpins help each other out

February 16, 2017

The evolution of cells and organisms is thought to have been preceded by a phase in which informational molecules like DNA could be replicated selectively. New work shows that hairpin structures make particularly effective DNA replicators.

In the metabolism of all living organisms there is a clear division of labor: Nucleic acids (DNA and RNA) carry the information for the synthesis of proteins, and proteins provide the structural and executive functions required by cells, such as the controlled and specific catalysis of chemical reactions by enzymes. However, in recent decades, it has become clear that this distinction is by no means absolute. In particular RNA is capable of ignoring the boundary outlined above and is known to play a catalytic role in many important processes. For example, certain RNA molecules can catalyze the replication of other nucleic acids, and this versatility could help to explain how life originated on Earth.

Nucleic acid molecules are made up of subunits called nucleotides, which differ in their so-called bases. The bases found in RNA are referred to as A, C, G and U (DNA uses T in place of U). These bases fall into two complementary pairs, whose members specifically interact, A with T (or U) and G with C. This complementarity is what accounts for the stability of the DNA double helix, and enables single strands of RNA to fold into complex shapes.

Life is thought to have emerged from a process of chemical evolution in which nucleic acid sequences could be selectively replicated. Thus, in prebiotic systems certain molecular "species" that carried information were reproduced at the expense of others. In biological systems, such selectivity is normally mediated by so-called primers -- strands of nucleic acid that pair (as described above) with part of the molecule to be replicated, to form a short double helix. The primer provides a starting point for the extension of the double-stranded region to form a new daughter strand. Moreover, this process can be reconstructed in the test-tube.

The pros and cons of hairpin replicators

Georg Urtel and Thomas Rind, who are members of the research group led by Dieter Braun (Professor of Systems Biophysics at LMU), have used such a system to identify properties the might favor the selective replication of DNA molecules. For their experiments, they chose a single-stranded DNA sequence that adopts a so-called hairpin structure. In these molecules, the base sequences at either end are complementary to each other, as are short stretches of sequence within the rest of the molecule. This distribution of complementary sequences causes such a strand to fold into a hairpin-like conformation.

Thanks to the pairing rules outlined above, replication of a single strand of DNA produces a second strand whose sequence differs from that of the first. Each strand of a non-hairpin structure therefore needs its own primer for replication. But with hairpins, one primer suffices to prime synthesis of both the original and its complementary strand. "This means that hairpins are relatively simple replicators," Georg Urtel points out. The downside is that the hairpin structure makes primer binding more difficult, and this in turn limits their replication rate. Molecular species that are devoid of hairpin structures don't have this problem.

Cooperation beats competition

In subsequent experiments the researchers discovered that two simple hairpin species could cooperate to give rise to a much more efficient replicator, which requires two primers for its amplification. The two hairpin species selected each required a different primer, but their sequences were in part identical. The switch to cooperative replication occurs when replication of one of the hairpins stalls. "As a rule, replication processes in nature are never perfect," says Dieter Braun. "Such a premature halt is not something that one needs to design into the system. It happens stochastically and we make use of it in our experiments." The partially replicated hairpin can, however, bind to a molecule of the second species, and serves as a primer that can be further elongated. Moreover, the resulting product no longer forms a hairpin. In other words, it represents a new molecular species.

Saved from extinction

Such so-called 'crossbreeds' need two primers for their replication, but can nevertheless be replicated significantly faster than either of their hairpin progenitors For further experiments showed that, upon serial dilution of the population, the hairpin DNAs soon become extinct. However, the sequence information they contained survives in the crossbreeds and can be replicated further.

The converse experiment confirmed that information is indeed conserved: If crossbreeds are supplied with only one primer, the corresponding progenitor hairpin species can still be replicated by the kind of switching process mentioned above. But, in the absence of the second primer, the crossbreed dies out. "Thus, the crossbreeding process not only provides for the transition from 'simple and slow' replicators to more rapid replicators, it also makes it possible for the system to adapt to the prevailing conditions," Urtel explains. "It also suggests how early replicators could have cooperated with each other under prebiotic conditions prior to the origin of living systems."

Ludwig-Maximilians-Universität München

Related Dna Articles:

Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.
In one direction or the other: That is how DNA is unwound
DNA is like a book, it needs to be opened to be read.
DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.
A new spin on DNA
For decades, researchers have chased ways to study biological machines.
From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.
Self-healing DNA nanostructures
DNA assembled into nanostructures such as tubes and origami-inspired shapes could someday find applications ranging from DNA computers to nanomedicine.
DNA design that anyone can do
Researchers at MIT and Arizona State University have designed a computer program that allows users to translate any free-form drawing into a two-dimensional, nanoscale structure made of DNA.
DNA find
A Queensland University of Technology-led collaboration with University of Adelaide reveals that Australia's pint-sized banded hare-wallaby is the closest living relative of the giant short-faced kangaroos which roamed the continent for millions of years, but died out about 40,000 years ago.
DNA structure impacts rate and accuracy of DNA synthesis
DNA sequences with the potential to form unusual conformations, which are frequently associated with cancer and neurological diseases, can in fact slow down or speed up the DNA synthesis process and cause more or fewer sequencing errors.
Changes in mitochondrial DNA control how nuclear DNA mutations are expressed in cardiomyopathy
Differences in the DNA within the mitochondria, the energy-producing structures within cells, can determine the severity and progression of heart disease caused by a nuclear DNA mutation.
More Dna News and Dna Current Events

Top Science Podcasts

We have hand picked the top science podcasts of 2019.
Now Playing: TED Radio Hour

Accessing Better Health
Essential health care is a right, not a privilege ... or is it? This hour, TED speakers explore how we can give everyone access to a healthier way of life, despite who you are or where you live. Guests include physician Raj Panjabi, former NYC health commissioner Mary Bassett, researcher Michael Hendryx, and neuroscientist Rachel Wurzman.
Now Playing: Science for the People

#543 Give a Nerd a Gift
Yup, you guessed it... it's Science for the People's annual holiday episode that helps you figure out what sciency books and gifts to get that special nerd on your list. Or maybe you're looking to build up your reading list for the holiday break and a geeky Christmas sweater to wear to an upcoming party. Returning are pop-science power-readers John Dupuis and Joanne Manaster to dish on the best science books they read this past year. And Rachelle Saunders and Bethany Brookshire squee in delight over some truly delightful science-themed non-book objects for those whose bookshelves are already full. Since...
Now Playing: Radiolab

An Announcement from Radiolab