<div><div>A new paper from the group of <a target="_blank" rel="noopener noreferrer" href="https://curtis.group.uochb.cz/en">Ed Curti</a>s at IOCB Prague in collaboration with the <a target="_blank" rel="noopener noreferrer" href="https://pluskal.group.uochb.cz/en">Pluskal group</a> introduces a structure-guided way to explore nucleic acid sequence space that goes far beyond traditional random mutagenesis. By combining rational library design, single-round selections, high-throughput sequencing, and machine learning, the authors rapidly identified catalytically active variants of a fluorescent deoxyribozyme and elucidated predictive rules linking sequence to function. The study was published in the journal Nucleic Acids Research.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/IOCB_Prague_Exploring_sequence_space_beyond_random_mutagenesis_2_2eb701e572.jpeg" alt="IOCB Prague: Exploring sequence space beyond random mutagenesis" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_IOCB_Prague_Exploring_sequence_space_beyond_random_mutagenesis_2_2eb701e572.jpeg 245w," sizes="100vw" width="2006" height="789"></div></div><div>Understanding how sequence determines function remains a central challenge in nucleic acid engineering. Conventional strategies typically rely on libraries generated by random mutagenesis of a single variant of a motif, which provide dense coverage close to the original sequence but little information about more distant variants. This limitation makes it difficult to uncover more general principles governing complex functional motifs such as catalytic nucleic acids.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/IOCB_Prague_Exploring_sequence_space_beyond_random_mutagenesis_e1e7a30d1c.jpg" alt="IOCB Prague/Tomáš Belloň: Edward Curtis, head of the Functional Potential of Nucleic Acids group at IOCB Prague" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_IOCB_Prague_Exploring_sequence_space_beyond_random_mutagenesis_e1e7a30d1c.jpg 234w," sizes="100vw" width="1500" height="1001">In a new study led by Edward A. Curtis, with Jaroslav Kurfürst and Martin Volek as the first authors, the researchers introduce a fundamentally different strategy for exploring sequence space that combines structure-informed library design, single-round selections, high-throughput sequencing, and machine learning. Instead of randomly mutating a single sequence, the team constructed a library composed of sequences that already satisfy multiple structural and functional constraints of a target motif. This approach was tested on Aurora, a fluorescent deoxyribozyme previously <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/4223">discovered</a> in the group.The results indicate that this approach is a more efficient way to explore sequence space than standard approaches. A secondary structure library based on Aurora yielded approximately 40 times more unique catalytic sequences than a conventional randomly mutagenized library, and active variants could be rapidly identified in a single round of selection. High-throughput sequencing data were then used to train machine learning models, which successfully identified rules relating sequence to activity. Remarkably, these models could accurately predict read numbers and identify the most active variants using only small subsets of sequences for training.By integrating rational library design with data-driven analysis, the study demonstrates a scalable way to explore nucleic acid sequence space more rapidly and comprehensively than standard methods allow. Beyond fluorescent deoxyribozymes, this framework provides a general blueprint for accelerating the discovery and optimization of functional nucleic acids, while simultaneously extracting predictive rules that link sequence to function.<blockquote><h5>Read the paper</h5>Kurfürst, J.; Volek, M.; Samusevich, R.; Pluskal, T.; Curtis, E. A. Using Structured Libraries, Selection, and Machine Learning to Rapidly Explore the Sequence Space of a Fluorescent Deoxyribozyme. Nucleic Acids Res. 2025, 53 (22). <a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1093/nar/gkaf1348">https://doi.org/10.1093/nar/gkaf1348</a></blockquote></div>

Exploring sequence space beyond random mutagenesis

Our Library never stops expanding. What are the most recent contributions to LabRulezGCMS Library in the week of 19th January 2026? Check out new documents from the field of the gas phase, especially GC and GC/MS techniques!<blockquote>👉 <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/library">SEARCH THE LARGEST REPOSITORY OF DOCUMENTS ABOUT GCMS AND RELATED TECHNIQUES</a></blockquote><blockquote>👉 Need info about different analytical techniques? Peek into <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library">LabRulezLCMS</a> or <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/library">LabRulezICPMS</a> libraries.</blockquote>This week we bring you application notes by Agilent Technologies, BaySpec and Metrohm!<h3>1. Agilent Technologies: Micro GC Analysis of Permanent Gas Impurities in PEM Fuel Cell-Grade Hydrogen</h3>According to SAE J2719, ISO 14687, EN 17124, and ISO 19880-8<ul><li>Application note</li><li><a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/an_micro_gc_analysis_gas_impurities_pem_fuel_5994_8830en_agilent_a5dca09e4b.pdf">Full PDF for download</a></li></ul>Quality requirements for hydrogen purity vary with application. Proton Exchange Membrane (PEM) fuel cell hydrogen is the application with the most stringent specification. Hydrogen purity specifications for other applications, i.e. residential or industrial use, typically allow for higher levels of specific&nbsp;contaminants.&nbsp;For PEM fuel cell-grade hydrogen, there are several key methods regulating quality. Some methods may also cover other scopes, but where they pertain to PEM fuel cell-grade hydrogen, they align on specific requirements for purity level and limit concentrations of specific contaminants.&nbsp;<ul><li>SAE J2719 specifies hydrogen fuel quality requirements for PEM fuel cell vehicles, such as hydrogen-powered cars.&nbsp;</li><li>ISO 14687 specifies minimum quality characteristics of hydrogen fuel for various applications, including residential, commercial, industrial, stationary systems, and vehicular use.&nbsp;</li><li>EN 17124 specifies the quality characteristics of hydrogen fuel dispensed at hydrogen refueling stations for use in PEM fuel cell vehicle systems.</li><li>ISO 19880-8 specifies the quality of the gaseous hydrogen at hydrogen distribution facilities and hydrogen fueling stations for PEM fuel cells for road vehicles.&nbsp;</li></ul>Micro GC is a suitable choice of technique for covering analysis of permanent gases in ultra high purity (UHP) hydrogen (oxygen, nitrogen, argon, helium, and methane). The small internal volume of the MEMS-based µTCD in the <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/library?manufacturerItems=1&amp;search=990+Micro+GC">Agilent 990 Micro GC</a> means that lower detection levels can be achieved when compared to regular TCDs, allowing for detection of contaminants in the single-digit ppm range. Note that ammonia, carbon monoxide, carbon dioxide, and formaldehyde can also be detected with Micro GC; however, additional/different columns might be required. Sensitivity requirements below 1 ppm may require alternate techniques.<h4>Experimental&nbsp;</h4>The method developed covers permanent gases defined in SAE J2719, and by default, also ISO 14687, ISO 19880‑8, and EN 17124. The <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/library?manufacturerItems=1&amp;search=990+Micro+GC">990 Micro GC</a> system was set up similar to the method described in Agilent application note 5994‑2138EN.1 A 20 m MS5A straight channel on hydrogen carrier gas was used. Table 2 lists experimental conditions for method development. A 20 m molsieve provides sufficient separation for the argon/oxygen peak pair at low-ppm concentrations.2 For best results, the column was operated at a low temperature of 30 °C. Hydrogen was used as carrier gas to completely mask the bulk hydrogen matrix peak, resulting in separation of the helium and neon baseline3 , while still allowing for a similar sensitivity as with the helium carrier. The hydrogen carrier allows helium (He), argon (Ar), oxygen (O2), nitrogen (N2 ), methane (CH4 ), and even neon (Ne) to be measured at their required levels. Carbon monoxide (CO) that elutes from the molsieve column is not part of the scope. SAE J2719 requires these to be measured at the sub-ppm level, which is too low for Micro GC. Table 3 lists the composition of calibration gas used. The system was calibrated using single‑point calibration.<h4>Conclusion&nbsp;</h4>The Agilent 990 Micro GC setup, described with a single 20&nbsp;m straight molsieve column running hydrogen carrier gas is capable of meeting the hydrogen quality requirement in SAE J2719 and other comparable UHP hydrogen methods for select permanent gases (He, Ar, O2, N2, CH4 ). The critical component, oxygen, can reliably be measured below the required five ppm level. Precision and accuracy are excellent for all components, and with a short runtime of five&nbsp;minutes, this analytical option can deliver 10–12 runs per hour. Detection of other components listed in SAE J2719, i.e.&nbsp;ammonia or CO/CO2 , will require different equipment.<h3>2. BaySpec: Detecting Toxins on Cannabis Leaves with Portable Miniature Mass Spectrometer</h3><ul><li>Application note</li><li><a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/Bay_Spec_App_Note_Toxin_Detection_on_Cannabis_Leaves_with_Portability_Mass_Spectrometer_b15213c47e.pdf">Full PDF for download</a></li></ul>Mass spectrometry in connection with different separa‐ tion techniques currently represents the main analytical approach for determination of residual pesticides in the Food &amp; Agriculture industry. Traditionally, samples need to be collected and sent to a laboratory for analysis using techniques such as GC‐MS or HPLC‐MS, which are costly and time‐consuming. In addition, the conventional mass spectrometer usually requires laborious sample pre‐ treatment, which does not allow for immediate in‐situ sample determination.Presented in this application note are data from a ther‐ mal desorption electrospray ionization (TD‐ESI) or atmso‐ pheric pressure chemical ionization (APCI) source coupled to a portable mass spectrometer for toxin screening of cannabis leaves.&nbsp;&nbsp;Bayspec’s <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/products/2219">Portability mass spectrometer</a> is less than 10 kg, highly portable, and battery‐operated.&nbsp;&nbsp;Its linear ion trap mass analyzer can perform fast in‐field detection of analytes, including residual toxins, by direct sampling of the surfaces of fresh food and plant products without any sample pre‐treatment.&nbsp;&nbsp;In this study, BaySpec’s sampling probe was used to directly swab the surface of cannabis leaves and inserted into the TD‐ESI or APCI sample inlet system for real time analysis. Four different samples were studied:&nbsp;<ul><li>Fresh cannabis leaves&nbsp;</li><li>Fresh cannabis leaves sprayed with PBO&nbsp;</li><li>Fresh cannabis leaves sprayed with myclobutanil&nbsp;</li><li>Fresh cannabis leaves sprayed with paraquat</li></ul>All sprayed samples were air‐dried prior to screening.&nbsp;&nbsp;No sample preparation was done to test the leaves.&nbsp;&nbsp;Both TD‐ ESI and APCI ionization methods tested positive for THC and toxins where applicable.&nbsp;&nbsp;See Figure 3 for recorded spectra.&nbsp;&nbsp;&nbsp;&nbsp;Due to short analysis times (1‐5 seconds per sample), this technique allows for fast screening for applications in food and environmental safety. MS (as well as MS/MS) analyses can be performed on surface‐residual toxins at parts per billion levels.&nbsp; &nbsp; The TD‐ESI ion source with PortabilityTM miniature mass spectrometer is available from BaySpec.&nbsp; &nbsp;&nbsp;This system does not require any add‐ itional support, external po‐ wer or gases. The simple in‐ tuitive software interface is operated by touch screen and makes the instrument ex‐ tremely easy to control. The external TD‐ESI source is fully integrated into the main software environment and the turn‐key system is user‐ friendly, does not require excessive training, and can be operated by persons with no previous mass spectrometry experiences<h3>3. Metrohm: Monitoring phosphate reactions in real time with Raman spectroscopy</h3><ul><li>Application note</li><li><a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/an_rs_054_download_d034c2ebb5.pdf">Full PDF for download</a></li></ul><h4>CURRENT METHODES FOR REACTION ANALYSIS</h4>Titration is highly effective for quantifying phosphate and sulfate species to determine reaction completion and final product composition in fertilizers. Gravimetric analysis is used to quantify insoluble byproducts like gypsum (CaSO4·2H2O). Both techniques require sample collection, hazardous reagents, and manual processing – all of which introduce time delays and incur costs with every measurement. This Application Note describes how Raman spectroscopy was used as an alternative method to monitor a simplified phosphate fertilizer production process under laboratory conditions.&nbsp;<h4>METHOD</h4><a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/library?mainauthorItems=220&amp;search=+i-Raman">Raman spectroscopy</a> is well suited to monitor phosphate species due to its high selectivity and nondestructive nature. Furthermore, it can simultaneously detect sulfate ions, enabling real-time analysis of multi-component reaction systems. In this study, dicalcium phosphate (CaHPO4, hereafter referred to as DCP) is used as a model compound for phosphate rock. In a 100 mL beaker, 500 mg of DCP was dissolved in 10 mL of 0.5 mol/L hydrochloric acid (HCl) (Equation 1). To simulate industrial reaction conditions and introduce sulfate ions, 0.25 mL of 1.0 mol/L sulfuric acid (H2SO4) was then added. The use of low-concentration HCl ensures safe handling and facilitates clear identification of the sulfate (SO42−) Raman peak.<h4>CONCLUSION</h4>Raman spectroscopy proved to be an effective tool for monitoring a phosphate fertilizer production process, providing clear insights into phosphate speciation, sulfate concentration, and precipitation dynamics. Raman spectral changes revealed transitions in phosphate protonation states and the formation of calcium-based precipitates. These capabilities support enhanced process control and product quality in phosphate fertilizer manufacturing.

News from LabRulezGCMS Library - Week 04, 2026

An international team of scientists, including experts from CATRIN at Palacký University, has developed a new type of plasmonic photocatalyst capable of converting biomass into key raw materials for bioplastic production with high efficiency and selectivity using solar energy. The research results, which represent a significant step towards more sustainable chemical manufacturing, have been published in the prestigious journal Nature Catalysis.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/CATRIN_A_new_generation_of_solar_catalyst_converts_biomass_into_raw_materials_for_bioplastics_e4dc54875b.jpg" alt="CATRIN: A new generation of solar catalyst converts biomass into raw materials for bioplastics" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_CATRIN_A_new_generation_of_solar_catalyst_converts_biomass_into_raw_materials_for_bioplastics_e4dc54875b.jpg 156w," sizes="100vw" width="1280" height="1280">Biomass—organic material of plant or animal origin—is among the most promising renewable resources for the production of high value-added chemicals and materials. The research focused on the molecule 5-hydroxymethylfurfural (HMF), which is derived from sugars contained in plant biomass and is regarded as one of the key intermediates in modern biorefineries. Through controlled oxidation, HMF can be converted into 2,5-furandicarboxylic acid (FDCA), a compound that serves as a fundamental building block for biopolymers, such as PEF plastic, an environmentally friendly alternative to the widely used PET.However, current industrial methods for producing this compound are technologically demanding. They often require strongly alkaline conditions, elevated temperatures, or increased pressure. Despite this, they suffer from low selectivity, leading to the formation of unwanted by-products and higher energy consumption. As a result, contemporary research is seeking new approaches that would allow this chemical transformation to be driven by light energy under milder and more environmentally friendly conditions.The newly developed catalyst is based on a combination of nanostructured titanium nitride and extremely small nanoparticles of a ruthenium–platinum alloy. Titanium nitride acts as a material that very efficiently absorbs light, particularly its infrared component, converting it into energy-rich electrons and local heat. These effects subsequently promote the activation of molecular oxygen on the surface of the catalytically active nanoparticles, where the chemical reaction itself takes place.“The key aspect is that the individual components of the catalyst work together in perfect synergy. This allows us to control the oxidation of 5-hydroxymethylfurfural with great precision and achieve an almost complete conversion to the target product without the use of strong chemical additives or extreme reaction conditions. Compared with existing technologies, the process is significantly more selective, more energy-efficient, and produces substantially less waste,” said one of the corresponding authors of the study, Štěpán Kment from Palacký University.The authors emphasise that this approach enables oxygen activation in a fundamentally different way than conventional catalytic systems. As a result, the reaction can be carried out in an aqueous environment without the addition of alkaline agents, while avoiding non-selective reactions that would otherwise lead to material losses. The outcome is a highly efficient and precisely controlled process suitable for future applications.According to the researchers, this plasmonic catalytic platform represents a previously unexplored concept in the field of biomass conversion. “It opens up new opportunities for future biorefineries that could use solar energy and renewable feedstocks to produce plastics, solvents, and other chemical products with a significantly lower carbon footprint than current industrial technologies,” concluded Kment.The research involved scientists from CATRIN at Palacký University, the Centre for Energy and Environmental Technologies, and the national supercomputing centre IT4Innovations at VSB–TUO, in collaboration with partners from China, Italy, and the United States.<blockquote><h4>The original article</h4><h4><a target="_blank" rel="noopener noreferrer" href="https://www.nature.com/articles/s41929-025-01454-y?fbclid=IwY2xjawOwzklleHRuA2FlbQIxMQBicmlkETBWZE9nUVBUR3ViTWs5ekptc3J0YwZhcHBfaWQQMjIyMDM5MTc4ODIwMDg5MgABHjMHx-lfljleJ5Hkgyj1B4u4IGXGChlp8YGVMWbdTjlmqC-beTiKrxofdB6H_aem_eS2PaVl3Ja6Hl0xfXYkHyw#Sec7">Near-infrared plasmonic activation of molecular oxygen for selective oxidation of biomass derivatives</a></h4>Manpreet Kaur, Sourav Rej, Jan Navrátil, Eva Yazmin Santiago, Michal Otyepka, Stefano Livraghi, Lorenzo Mino, Štěpán Kment, Zhikang Xu, Haibo Zhu, Paolo Fornasiero, Alexander O. Govorov, Piotr Błoński &amp; Alberto NaldoniNat Catal 8, 1370–1381 (2025)<a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1038/s41929-025-01454-y">https://doi.org/10.1038/s41929-025-01454-y</a><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a></h6></blockquote>Selected sections from the article follow. Formats and hyperlinks were adapted from the original.<h4>Abstract</h4>Upgrading biomass feedstock into higher-value chemicals is central to improve the sustainability of the chemical industry and to reduce its dependence on fossil raw materials. Heterogeneous photocatalysts are promising for the oxidation of 5-hydroxymethylfurfural (HMF) to 2,5-furandicarboxylic acid (FDCA), a biomass-derived molecular platform for biopolymers, but their FDCA selectivity is negligible without the aid of a base. Here we present a plasmonic photocatalyst integrating TiN nanocubes and bimetallic RuPt nanoparticles that in base-free conditions exhibits complete HMF conversion and selective FDCA formation due to an unconventional mechanism of molecular oxygen activation. This unique reactivity is enhanced by both photothermal heating and hot electrons, whose contribution is confirmed by kinetic isotopic effect experiments. Density functional theory calculations support a scenario in which the activated nanoparticle–oxygen complex facilitates the rate-determining step and enables an improved FDCA selectivity. Our results demonstrate the potential of plasmonic photocatalysts in the catalytic transformation of biomass.

A new generation of solar catalyst converts biomass into raw materials for bioplastics

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Toxicology

Science and research

The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague) is a leading scientific institution in the Czech Republic, recognized internationally. Its primary mission is basic research in the fields of chemical biology and medicinal chemistry, organic and material oriented chemistry, chemistry of natural compounds, biochemistry and molecular biology, physical chemistry, theoretical chemistry, and analytical chemistry. 

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

The Czech Advanced Technology and Research Institute (CATRIN) at Palacký University is a cutting-edge scientific hub dedicated to advancing research in the fields of nanotechnology, biotechnology, and biomedicine. At its core, CATRIN boasts outstanding scientific teams, featuring international researchers. We emphasize interdisciplinarity, foster global collaborations, and work to translate our research findings into practical applications.

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A new generation of solar catalyst converts biomass into raw materials for bioplastics

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News from LabRulezGCMS Library - Week 04, 2026