DNA – Lightsources.org

Organic matter found in 44-million-year-old beetle fossil

2023/04/192023/05/03

Remember Jurassic Park? The dinosaurs in that movie franchise were brought to life through DNA found in amber. The DNA purportedly came from mosquitoes that had taken blood from dinosaurs prior to being trapped in the tree resin that turned into amber.

Amber, a semi-precious stone that is fossilized tree resin, often contains the fossilized remains of insects and other small creatures, with little, if any, organic matter left. No organic matter, no dinosaur DNA, no Jurassic Park.

However, a team of researchers from the University of Regina, Royal Saskatchewan Museum, and Institute of Life Sciences and Technologies at Daugavpils University in Latvia, have now identified what appears to be organic matter in a 44-million-year-old beetle fossilized in amber.

This remarkable finding, and the methodology used in making it, has been published in Nature’s Scientific Reports, the fifth most-cited journal in the world.

“Using a set of advanced techniques we’ve not tried before, we took a 44-million-year-old beetle trapped in Baltic amber to see if it was possible that any preserved organic material might be present,” says U of R master’s of science student Jerit Mitchell, lead author of the study.

Dr. Mauricio Barbi, a U of R physics professor, says the team used the synchrotron radiation facilities at the University of Saskatchewan’s Canadian Light Source (CLS) in Saskatoon to extract high-resolution 3D micro-computed tomography (micro-CT) images of the beetle.

“The synchrotron mid-infrared radiation gave us the capability to identify possible organic compounds in the specimen. We then complemented these two synchrotron radiation techniques by using a scanning electron microscope to provide further high-resolution images of the beetle and to determine the specific chemical elements present in the sample,” says Barbi, who led the team that discovered structurally preserved fossilized dinosaur cell layers in the skin of a 72-million-year-old hadrosaur.”

Read more on the website

Image: Jerit Mitchell gazing at a millions-year-old fossilized beetle

Credit: U of R Photography

Targeting a parasite’s DNA could be more effective way to treat malaria

2022/08/082022/08/11

Research from the University of Sheffield using Diamond has explored a new way of killing the Plasmodium parasite that causes malaria.

According to the World Health Organisation, there were 241 million cases of malaria and 627,000 deaths worldwide in 2020 – making the study and treatment of this disease a high-priority issue for scientists around the world. In a feasibility study, researchers from the University of Sheffield used Diamond to reveal a novel way of fighting the life-threatening disease, malaria. The study discovered molecules that interfered with the parasite’s DNA processing enzyme, but not the equivalent human one.

A research team from the University of Sheffield’s Department of Infection, Immunity and Cardiovascular Disease examined and targeted an enzyme that maintains the classic double-helical structure of the malaria parasite’s DNA, which contains the blueprint of life, which could be a more effective way to combat malaria.

Read more on the Diamond website

Image: A flap endonuclease cuts DNA (the orange intertwined worms), credit University of Sheffield

Searching for the chemistry of life

2020/10/022020/10/08

Study shows possible new way to create DNA base pairs

In the search for the chemical origins of life, researchers have found a possible alternative path for the emergence of the characteristic DNA pattern: According to the experiments, the characteristic DNA base pairs can form by dry heating, without water or other solvents. The team led by Ivan Halasz from the Ruđer Bošković Institute and Ernest Meštrović from the pharmaceutical company Xellia presents its observations from DESY’s X-ray source PETRA III in the journal Chemical Communications.

“One of the most intriguing questions in the search for the origin of life is how the chemical selection occurred and how the first biomolecules formed,” says Tomislav Stolar from the Ruđer Bošković Institute in Zagreb, the first author on the paper. While living cells control the production of biomolecules with their sophisticated machinery, the first molecular and supramolecular building blocks of life were likely created by pure chemistry and without enzyme catalysis. For their study, the scientists investigated the formation of nucleobase pairs that act as molecular recognition units in the Deoxyribonucleic Acid (DNA).

Read more on the PETRA III (DESY) website

Image: From the mixture of all four nucleobases, A:T pairs emerged at about 100 degrees Celsius and G:C pairs formed at 200 degrees Celsius. Credit: Ruđer Bošković Institute, Ivan Halasz

First structure of a DNA crosslink repair ligase determined

2019/11/042019/11/05

Diamond’s Electron Bio-Imaging Facility (eBIC) has been used to generate the first 3D structure of the Fanconi anaemia (FA) core complex, a multi-subunit E3 ubiquitin ligase required for the repair of damaged DNA. The work, led by Dr Lori Passmore from the MRC Laboratory of Molecular Biology and a team of researchers, has been published today in Nature, and their research provides the molecular architecture of the FA core complex and new insights into how the complex functions.

The FA pathway senses and repairs DNA crosslinks that occur after exposure to chemicals including chemotherapeutic agents and alcohol, but also as a result of normal cellular metabolism. The megadalton FA core complex acts as an E3 ubiquitin ligase to initiate removal of these DNA crosslinks, helping to repair the damage caused. The research team used eBIC’s imaging facilities to make a major breakthrough in understanding the FA core complex by determining its structure using an integrative approach including cryo-electron microscopy and mass spectrometry.

Dr Peijun Zhang, Director of eBIC notes that:

Enabling cutting-edge research like this is exactly why we established eBIC, to provide scientists with state-of-the-art experimental equipment and expertise in the field of cryo-electron microscopy, for both single particle analysis and cryo-electron tomography. Determining the structure of the FA core complex for the first time is a fantastic achievement for the MRC research team.

Image: The FA core complex.
Credit: Phospho Biomedical Animation

Mechanism of thiopurine resistance in acute lymphoblastic leukemia

2019/02/282019/03/13

Acute lymphoblastic leukemia (ALL) is an aggressive lymphoid malignancy that is currently the leading cause of cancer in pediatric patients¹. Despite intensified chemotherapy regimens, the cure rates of ALL only approaches 40%². Specific mutations in the cytosolic 5’-nucleotidase II (NT5C2) gene are present in about 20% of relapsed pediatric T-ALL and 3-10% of relapsed B-precursor ALL cases^3,4.

NT5C2 is a cytosolic nucleotidase that maintains intracellular nucleotide pool levels by exporting excess purine nucleotides out of the cell⁵. NT5C2 can also dephosphorylate and inactivate the metabolites of the 6-thioguanine (6-TG) and 6-mercaptopurine (6-MP) commonly used to treat ALL⁶. Thus, relapse associated activating mutations in NT5C2 confer resistance to 6-MP and 6-TG chemotherapy. Upon allosteric activation, a disordered region of NT5C2 adopts a helical configuration (helix A) and facilitates substrate binding and catalysis (Fig. 1a)⁷. Mutations in this regulatory region of NT5C2 have been modeled to strongly activate NT5C2. However, the majority of NT5C2 mutations associated with relapsed ALL do not occur in this region.
To better understand the mechanisms by which these gain-of function NT5C2 mutations lead to increased nucleotidase activity, Dieck, Tzoneva, Forouhar and colleagues investigated additional regulatory elements that may control NT5C2 activation. They collected crystallographic data for several mutant NT5C2 homotetramers at SSRL (NT5C2-537X D52N/D407A in active state (BL9-2), NT5C2-Q523X D52N in basal state and in active state (BL14-1) and full-length NT5C2 R39Q/D52N in basal state (BL12-2)) and used the structural information as a guide in the understanding of the mechanistic details.

Figure (a) A ribbon diagram of the active structure of NT5C2 WT, in which the allosteric helix A (αA) is shown in dark purple. The N and C termini amino acids (S4 and S488), and the termini amino acids (L402 and R421) of the disordered region in the arm segment are also labeled. Panels b and c shows ribbon and surface (for subunit B) depictions of basal (b) and active dimers (c) of WT.

New forensic DNA profiling technique on the horizon

2018/06/082018/06/18

A study recently conducted at the Circular Dichroism beamline (B23) here at Diamond Light Source could pave the way to a new forensic DNA profiling technique. Researchers hailing from the Ivanovo State University of Chemistry and Technology, Russia, The University of Southampton and Diamond investigated the application of specially designed DNA building blocks.

DNA is a versatile template that can be used for a variety of applications. It is made up of building blocks known as nucleotides (labelled A, C, G and T) which form long strands that bind to complementary sequences and give the familiar double helix. The nucleotides can be tailor made to build new functional molecules for biotechnology, analytics, or even materials science.

Structural Mechanisms of Histone Recognition by Histone Chaperones

2018/02/282018/03/08

Chromatin is the complex of DNA and proteins that comprises the physiological form of the genome. Non-covalent interactions between DNA and histone proteins are necessary to compact large eukaryotic genomes into relatively small cell nuclei. The nucleosome is the fundamental repeating unit of chromatin, and is composed of 147bp of DNA wrapped around an octamer of histone proteins: 2 copies of each H2A, H2B, H3 and H4.

Assembly of nucleosomes in the cell requires the coordinated effort of many proteins including ATP-dependent chromatin remodeling enzymes and ATP-independent histone chaperone proteins. Histone chaperones are a large class of proteins responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating nuclear import of histones, and finally depositing histones onto DNA to form nucleosomes. Despite performing many overlapping functions, histone chaperone proteins are highly structurally divergent. However, nearly all histone chaperones contain highly charged intrinsically disordered regions (IDRs)¹. In many cases truncation of these conserved regions results in loss of histone affinity and deposition functions.

Image: (extract) SAXS analysis of Npm Core+A2 truncation (1-145) bound to five H2A/H2B dimers. Left: small angle x-ray scattering curve of the complex (purple dots). Simulated SAXS curve from the best scoring structural model shown as a black line. Right: SAXS envelope of the complex (pink) with the best scoring structural model inside. Positioning of H2A/H2B dimers by NMR and SAXS structural restraints. Full image here.

Molecular Movie

2017/08/192017/10/12

Researchers Create Molecular Movie of Virus Preparing to Infect Healthy Cells

With SLAC’s X-ray laser, scientists captured a virus changing shape and rearranging its genome to invade a cell.

A research team has created for the first time a movie with nanoscale resolution of the three-dimensional changes a virus undergoes as it prepares to infect a healthy cell. The scientists analyzed thousands of individual snapshots from intense X-ray flashes, capturing the process in an experiment at the Department of Energy’s SLAC National Accelerator Laboratory.

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