Nav: Home

In one direction or the other: That is how DNA is unwound

October 30, 2019

From home to office and back. The road is the same, and yet the outbound journey is longer than the inbound journey. Why is that? The reason is the obstacles the car driver usually finds on his way to work, which are absent on the way back. Now, replace the road with DNA strands and you will have grasped the crux of the discovery just published by an international research group on the journal PNAS. The double helix of DNA is subject to the action of specific proteins, called helicases, which have the task of separating the two strands so that the information contained in the genome is made available for a variety of activities that are essential to cell life. In short, DNA is like a book, it needs to be opened to be read! Helicases have the task of opening this "book". Through this work, the researchers have shown that helicases succeed in carrying out their task more easily, and therefore quickly, working on one of the two strands with respect to the other. They explained that the reason lies in the sequence composition of the DNA section. As we know, DNA has four nitrogenous bases, which constitute the alphabet that is used to write our genome. When there are "hindered" bases like adenine and guanine on the strand opposite to that on which the helicase moves, they bump against the helicase and make the process slower. If, on the contrary, there are "small" bases, like cytosine and thymine, the opening process is faster. The scientists infer that this could mean that the genome has yet-another way, which has not been considered until now, of regulating the flow of information: indeed, the genetic information connected with the direction in which the helicase proceeds more slowly will be read less frequently - with possible consequences on the gene expression. The research was initially conducted with computer simulations. The predictions obtained in this manner were then confirmed by experiments. The study emerged from an idea of two SISSA scientists, Professor Giovanni Bussi and Francesco Colizzi, who has since moved to the Institute for Research in Biomedicine (IRB Barcelona), Spain, and has involved the laboratories led by Carlos Penedo and Malcolm White at the University of Saint Andrews, Great Britain, with their collaborators.

First theory and then experiment

"We know that the difficulty in unwinding a double strand of DNA or RNA depends on the strength which binds the two, but that the same double helix was easier to unwind in one direction rather than the other has been a real surprise. We have come to propose this hypothesis through computer simulations and subsequently designed real lab experiments that could prove or disprove the hypothesis. Eventually, the lab experiments proved that the hypothesis was correct". Thanks to fluorescent tracers, the researchers observed that in the experiment the double helix is processed more easily in one direction rather than the other". In short, there is one strand and one preferential direction for unwinding DNA according to the message written in it. Scientifically, this is very interesting". Since the helicase opens the double helix moving on a strand separating it from the opposite one, "we have hypothesised and verified that the speed of this process depends on the composition of the bases of the latter". If there are many bumpy bases, like guanine and adenine, then the helicase will have a more complex task and proceed more slowly. And vice versa. "What we can say is that the direction with which it is easier to separate a double helix depends on the sequence of bases in a specific region".

The implications of the discovery

This discovery bears different points of interest. The first, as we said, is connected with the approach that brings together computer simulations and lab experiments in a combination that leads us straight to the frontiers of science. The second is of a more general nature: "The regulation of all the activities in which DNA is involved is one of the most interesting and crucial issues of biology, in which much more still needs to be discovered. With this study we put forward a hypothesis that has not been considered so far: namely, that the various types of regulation already known are joined by another which relates specifically to the preferential direction in which a double strand is read, based on the ease of being unwound. There is an additional, more speculative consideration, based on the observation that DNA unwinds in a different way to RNA. "For DNA, we find helicases able to work in both directions. Instead, for RNA, the helicases found in nature follow mostly one-way roads. The hypothesis of the scientists is that the double helix of RNA has some sort of geometrical asymmetry (different to DNA) that, throughout evolution, has dictated the one-way direction of RNA helicases. It can therefore be speculated that evolution has selected the helicases that processes RNA in the direction in which it is easy to travel. Unfortunately, a hypothesis of this kind cannot be refuted or verified: to do so, it would be necessary to retrace the natural evolution for millions of years, eliminating this preference and seeing what happens! It is definitely fascinating to think that the geometry of the double helix can have deeply influenced the development of molecular machines necessary for life."
-end-


Scuola Internazionale Superiore di Studi Avanzati

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