Building blocks of life under UV irradiation

To begin with

Photochemists have managed to study in depth the behaviour of the DNA and RNA components called ‘bases’, which are fundamental for life on Earth, when these are exposed to ultraviolet light. This has been possible only due to the development of state-of-art laser spectroscopy enabling the observation of very fast processes.

Keywords

Femtochemistry, Spectroscopy, Ultraviolet (UV) light, DNA bases, DNA damage, Excitation, Light Absorption, Photon, Femtosecond laser

About

Photochemists at the Francis Perrin Laboratory (FPL) focus part of their research on five small molecules, called bases that are fundamental components of the DNA and RNA macro-molecules. Specifically, they study the way these bases behave when exposed to ultraviolet light (UV). (watch Dr. Gustavsson explaining why they focus on UV light)

Until the beginning of the 21st century, it was already known that when these five bases absorb ultraviolet light, they are brought to a so called “excited state”, but very rapidly shrug off the excess energy to the environment. The time that the base remains in the excited state, i.e. the excited state ‘lifetime’, turns out to be extremely short and it couldn't be precisely determined for a long time because it was technically too difficult a task.

This was finally achieved thanks to the development of  ultrafast laser spectroscopy experiment. Since 2001, photochemists at the FPL managed to measure this extremely short lifetime of the excited states of the DNA and RNA bases. (watch Dr. Gustavsson talking about the ultrafast deactivation of the DNA molecule)

After this first achievement, the researchers tried to understand the detailed mechanism that enables this unusually ultrafast evacuation of the excess energy possible.

Links with society

Research on individual DNA and RNA bases, could contribute to different aims with a variety of applications.

1. Scientists understand better how building blocks of life such as DNA and RNA bases, survived in the harsh environment of Earth before the emergence of Life as we know it. At that time, intense ultraviolet irradiation was reaching Earth, partly due to the lack of the protective ozone layer of the atmosphere, as it is now.
2. We gain knowledge about the very first steps preceding the carcinogenic mutations induced by UV light. (watch Dr. Gustavsson explaining how UV light can cause cancer) To this end, scientists compare the behaviour of the bases when organised within a DNA double helix with that of the individual bases.
3. The knowledge of the behaviour of DNA or RNA bases when irradiated by UV light is a prerequisite for their integration as building blocks in molecular electronic and optoelectronic devices. This is a new perspective appeared quite recently.
4. Due to the very short lifetime of the excited state of the DNA and RNA bases, the researchers can use them as models to understand the ultrafast excitation process of other molecules.

Research innovation

What’s new?

The group of scientists at the Francis Perrin Laboratory (FPL) was one of the first that succeeded in measuring the time needed for the DNA and RNA bases to release the excitation energy acquired by absorption of ultraviolet light. This process, called excited stated relaxation, takes place in less than one picosecond, which is a very very small fraction of time. But the researchers want also to understand the mechanism that enables the relaxation process to occur so rapidly. (watch Dr. Gustavsson talking about the research project)

At the FPL the DNA or RNA bases are studied in solutions, most often in water. After absorbing light energy, a base starts folding itself until it releases the excitation energy which is transferred to the environment, i.e. the solvent molecules. During these processes, various modifications happen in the electronic structure of the base and its relation to the surrounding solvent molecules. These changes are described under the complicated concept of “conical intersection”.

The fact that the cycle of absorption - release of light energy happens with very high speed decreases the probability that the base undergoes chemical reactions. This gives the base a kind of resistance against UV irradiation, which could explain the natural ‘selection’ of these chemical compounds as building blocks of life. (watch Dr. Gustavsson explaining how the DNA bases get rid of the excess energy)

Description of the method

The natural phenomena to be studied guide the scientists into selecting the most fitted methodological resources, technologies and instruments and inspire the appropriate use of theoretical models closely combined with the experimental work. (watch Dr. Gustavsson explaining how they proceeeded in order to study the DNA molecule as a whole)

Focusing on the experiments
One of the most characteristic features of this study is the ultrafast speed of the processes under scrutiny which made it necessary for the scientists to develop specific experimental setups. (watch Dr. Gustavsson talking about the laser equipments)

Use the right lasers
Scientists use femtosecond lasers in order to shine light (energy) on a base molecule over a very short period of time, which typically is 100 femtoseconds. One femtosecond (10-15 s) is a billionth of millionth of a second! It is so short that its timespan is nearly impossible to perceive. By way of example, one may think of the femtosecond compared to a second as the thickness of a human hair to the distance between the earth and the moon. Therefore, it is well suited to study the rapid processes of excitation/relaxation of a base. (watch Dr. Gustavsson talking about the type of laser pulses used at the experiments)

Study the average excitation/relaxation time of the DNA/RNA bases
In order to determine the lifetime of the exited state, researchers take advantage of the fact that excited molecules emit light (fluorescence). Thus, they shine light on bases and study how long it takes for the fluorescence to fade out.

Theory informs experimentation and vice versa
Generally talking, the “nature” of a molecule, excited or not, can be described by theoretical model calculations. In the case that the theoretical predictions match the experimental ones, then the theoretical model makes sense. New experiments are designed in order to examine whether the theory describes correctly the molecular movements of each base in its excited state as well as its interaction with the surrounding solvent molecules. (watch Dr. Gustavsson talking about the study of model systems)
There are two categories of experiments. In the first category, we replace for example, a hydrogen atom by a methyl group, or a halogen atom. In the second category, we replace the substance of the solvent, e.g. change the water to alcohol. According to the theoretical model, these interventions are expected to have a certain effect to the lifetime of the excited base. If this expectation fails then the theoretical model has to be revised.

(Press here to watch a series of animated drawings on Femtochemistry created by FUB)

Historical background

Going back to the roots…
Before we start talking about the interaction between UV radiation and DNA bases, we should first think of the great moments in the history of science and technology that allowed scientists today to deal with such complicated notions. It wasn’t always known that the key for the development of a cell and consequently of an organism, was hidden in the DNA molecule. Moreover, it wasn’t until 1953 when James Watson and Francis Crick presented the structure of the DNA-helix. The findings of their famous scientific paper were based on the work of Rosalind Franklin, a British biophysicist who died some years later. Her historical “photograph 51” with X-ray crystallographic methods helped in revealing the complexities of the most important biomolecule. 
On the other hand, one of the most important tools that modern technology provides to the scientists for studying the very basic parts of our genetic code, the lasers, have been invented just over 50 years ago. Theodore Maiman, an American physicist, was the first who constructed and demonstrated in 1960 an operable laser using a cylinder made of ruby. At the time of its invention, Maiman's laser was referred to by some as a “death ray”, despite the fact the scientist himself had commented its use in developing weapons systems as most unlikely. Today, lasers are present in numerous daily-life activities, from CD and DVD players to telecommunications, and from eye surgery to industrial metal manufacturing and treatment. 

The "face" of Science: Let's meet the scientists!

Scientists at the Francis Perrin Laboratory (LFP) have highly contributed to the understanding of what happens in the DNA molecule directly after it has absorbed an ultraviolet (UV) photon. (watch Dr. Gustavsson explaining how the study of individual bases can help to understand the behaviour of the whole DNA molecule)

But, who are these people working behind the scenes?

The “face” of science: Dr. Thomas Gustavsson, CNRS Research Director

Brief introduction
Being an experimentalist, Thomas Gustavsson has a long experience in laser spectroscopy. A Swedish citizen, he received his PhD in physics at the University of Stockholm (Sweden) in 1988 in the field of high-resolution molecular spectroscopy. He moved to France in 1988 and entered CNRS in 1991 to work in condensed phase photophysics and photochemistry.

Research interests
Thomas Gustavsson has developed and applied various laser-based picosecond and femtosecond spectroscopic setups dedicated to the study of molecular excited states dynamics since 1991. Having tackled various "ultrafast" topics, such as solvation dynamics, electron and proton transfer reactions as well as the dynamics of higher electronic states, he focuses his efforts, since the foundation of Francis Perrin Laboratory in 2000, on DNA photochemistry. He has in particular developed a unique "fluorescence upconversion" setup allowing the study of the very weak DNA fluorescence which requires excitation and detection in the UV spectral region. (watch Dr. Gustavsson talking about his research interests)

Sources of inspiration
Thomas Gustavsson has been "in the right place at the right time". In the early 90s, modern, reliable femtosecond lasers were just starting to be commercialized. During that period he had the great opportunity to start a femtosecond laser laboratory in collaboration with some enthusiastic colleagues, post docs and PhD students. Just about everything remained to be discovered and there was a lot of excitement everywhere, in France as well as in the rest of the world.

Important moments in his “scientific life”
Thomas Gustavsson remembers in particular a very heated debate that occurred at the CLEO conference in Baltimore in 1990. This discussion, which involved, among others, W. Sibbett, Professor at St. Andrews University, Scotland and W. Knox from Bell Labs, concerned the mechanism behind the recently discovered (at that time) "magic mode-locking" of titanium sapphire lasers allowing the generation of 100 fs pulses. To be present at such a vivid round table debate and actually see how science is formulated in "real time" is a rare but extremely encouraging experience. Another occasion that springs to his mind was meeting and discussing with A. Zewail, Nobel Prize winner in Chemistry in 1999, who also coined the term "Femtochemistry". The fertility of Prof. Zewail's mind, leaping ahead in every direction, is a very inspiring thing to see "in action".

Research team behind the scenes
Thomas Gustavsson is active in a small research team at the FPL, the Excited Biomolecules Group.
Apart from himself, this group is constituted by Dimitra Markovitsi, Head of the Francis Perrin Laboratory and the Excited Biomolecules Group, Pascale Changenet-Barret and Akos Banyasz, CNRS research scientists and Marion Perron, a young CNRS technician. There is an invited  Italian scientist, Roberto Improta and a Spanish post-doctoral researcher, Ignacio Vaya.
This multi-national and multi-cultural environment, typical for CNRS, plays a key role in the very productive research performed in the Excited Biomolecules Group.

Editing team

Editing Team for the exhibit “Building blocks of life under UV irradiation”:

Scientific editors: Thomas Gustavsson (leader of this particular research project), Dimitra Markovitsi (Research Director at FPL)

Content Coordination: Glykeria Anyfandi
Science Communication Editors: Evlalia Amygdalaki, Glykeria Anyfandi
Content Administration: Christina Troumpetari, John Stoitsis
Technical Development: John Stoitsis

Animation and ICT material: CediS, Free University of Berlin

Cartoons: Ghislain Aubry (design), Dimitra Markovitsi (scenario)
Photographs, videos & web material: Evlalia Amygdalaki
e-Knownet Live experiments: Interactive Science & Technology Exhibition, Eugenides Foundation