Article
Biochemical Research Methods
Matthew J. Sorensen, Mellie June Paulines, Todd D. Maloney
Summary: This study evaluated the orthogonality between ion-pair reversed phase (IP-RP), anion exchange (AEX), and hydrophilic interaction liquid chromatography (HILIC) for the separation of oligonucleotides. The results showed that coupling HILIC with either AEX or IP-RP provided the highest degree of orthogonality.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Multidisciplinary
Niu Wenxue, Liu Zheyi, Liu Jing, Lai Can, Zhang Tingting, Zhao Heng, Wang Guosheng, Wang Fangjun
Summary: High-resolution liquid chromatography separation is crucial for in-depth proteomic profiling. The IPRPxRP 2DLC strategy established in this study showed improved separation efficiency and increased peptide identification compared to conventional high-pH RP fractionation.
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES
(2023)
Article
Chemistry, Multidisciplinary
Liudan Jiang, Jiayong Yin, Maoxiang Qian, Shaoqin Rong, Shengqi Zhang, Kejing Chen, Chengchen Zhao, Yuanqing Tan, Jiayin Guo, Hao Chen, Siyun Gao, Tingting Liu, Yi Liu, Bin Shen, Jian Yang, Yong Zhang, Fei-Long Meng, Jinchuan Hu, Honghui Ma, Yi-Han Chen
Summary: In this study, a Ucaps-seq method was developed to detect uracil in DNA at single-nucleotide resolution. The method was proven to be highly specific and effective on synthetic DNA and real genomes. Ucaps-seq not only detected the enrichment of uracil in cells but also had potential applications in evaluating base editing fidelity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Feiyang Li, Michael Laemmerhofer
Summary: A short RNA sequence was selected as test material to investigate common impurities using three different 2D-LC platforms, allowing for sensitive ESI-TOF-MS analysis of impurity peaks under MS-friendly conditions. The methods demonstrated the potential for comprehensive impurity profiling of ON therapeutics through selective sampling and high-resolution separation. Online coupling of different LC modes in the second dimension enabled the separation of additional impurities that coeluted in the first dimension.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Biochemical Research Methods
Martin Gilar, Brooke M. Koshel, Robert E. Birdsall
Summary: This study investigated the separation of a fully phosphorothioated oligonucleotide from its truncated n-1 species and selected phosphodiester impurities using ion-pair reversed-phase chromatography. The hydrophobicity of ion-pairing agents impacts the separation selectivity of n-1 species. The study found that hydrophilic interaction chromatography provided a different retention pattern and improved the chromatographic separation of the truncated and phosphodiester impurities.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemistry & Molecular Biology
Kasper K. Sorensen, Narendra K. Mishra, Maciej P. Paprocki, Amit Mehrotra, Knud J. Jensen
Summary: The study investigated the use of high-performance reversed-phase flash chromatography (HPFC) for rapidly purifying laboratory-scale quantities of crude, synthetic peptides and chemically modified insulins, demonstrating its versatility for various types of peptides. Depending on the peptide's purity profile, HPFC can serve as a standalone purification method or as a pre-purification step before final HPLC purification, providing guidelines for synthetic peptides and small proteins. HPFC is considered a valuable alternative to HPLC purification for peptides and small proteins.
Article
Biochemical Research Methods
Tomoka Yoshii, Akihiro Sakama, Kazuyoshi Kanamori, Kazuki Nakanishi, Hiroaki Imai, Daniel Citterio, Yuki Hiruta
Summary: This article presents a study on an alkali-resistant reversed-phase packing material prepared from eggshells modified with an amphiphilic copolymer for purification of basic drugs. The material showed good selectivity and retention performance, making it effective for purifying alkaline drugs and acid-sensitive compounds.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Analytical
Marilyn De Graeve, Emma Van de Walle, Thomas Van Hecke, Stefaan De Smet, Lynn Vanhaecke, Lieselot Y. Hemeryck
Summary: Although the field of DNA adductomics is still in its infancy, this study evaluated different methods for sample analysis and data processing. The results showed that hydrophilic interaction coupled with high resolution mass spectrometry and thermal acidic hydrolysis in combination with solid-phase extraction provided better results for studying DNA adducts. Furthermore, quality control normalization was found to be more effective compared to other normalization strategies. Therefore, quality control normalization can be recommended as the default data normalization strategy.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Zuzana Kadlecova, Kveta Kalikova, Eva Tesarova, Martin Gilar
Summary: Ion-pairing reversed-phase liquid chromatography was used to analyze native and phosphorothioate oligonucleotides with the same sequence but different amount and position of modifications. The nature and concentration of ion-pairing amines were found to significantly impact the retention, resolution, and diastereomeric separation of the oligonucleotides. Increasing hydrophobicity and concentration of ion-pairing amines improved the resolution of n and n-1 mers oligonucleotides, while amines with moderate hydrophobicity were most successful in suppressing diastereomeric resolution. However, a partial separation of phosphorothioate oligonucleotide diastereomers was observed with all ion-pairing systems, resulting in wider peaks compared to phosphorodiester oligonucleotides of the same sequence. The separation of oligonucleotides with different number of phosphorothioate modifications may be useful for therapeutic oligonucleotide analysis.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biochemical Research Methods
Zuzana Kadlecova, Kveta Kalikova, Eva Tesarova, Martin Gilar
Summary: The analysis of diastereomers of phosphorothioate oligonucleotides in ion-pairing reversed-phase liquid chromatography is influenced by the ion-pairing system, concentration, and temperature. This study investigated the effects of temperature on retention, diastereomeric separation, and resolution of mers of different length and phosphorothioate oligonucleotides with different linkages. The results showed that increased temperature suppresses diastereomeric separation but improves the resolution of n and n-1 mers.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biochemical Research Methods
Feiyang Li, Shenkai Chen, Sylwia Studzinska, Michael Laemmerhofer
Summary: With the increasing use of nucleic acid-based pharmaceuticals, efficient analytical methods are needed for synthetic oligonucleotides. Two-dimensional chromatography techniques, including orthogonal chromatographic methods, are becoming more relevant due to the complexity of the oligonucleotides. In this study, a new polybutylene terephthalate-based stationary phase was tested for the analysis of siRNA, showing higher orthogonality and improved resolution for peak purity evaluation.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemical Research Methods
Abdul Haseeb, Maria Rova, Jorgen Samuelsson
Summary: An analytical method was developed for the determination of tributylamine (TBuA) and triethylamine (TEtA) in chromatographic mobile phase, and the adsorption isotherms of tributylammonium acetate (TBuAA) and triethylammonium acetate (TEtAA) were obtained using the same method. The adsorption behaviors of TBuAA and TEtAA showed type III and type I isotherm behavior, respectively.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Review
Chemistry, Multidisciplinary
Hana Dohnalova, Filip Lankas
Summary: The review article discusses recent developments in modeling the mechanical properties of DNA in its B-form, using various models and molecular dynamics simulations. The models are illustrated and critically examined using MD data and Amber force fields.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Cheng-Jie Ma, Lin Li, Wen-Xuan Shao, Jiang-Hui Ding, Xiao-Li Cai, Zhao-Rong Lun, Bi-Feng Yuan, Yu-Qi Feng
Summary: 5-Hydroxymethyluracil (5hmU) is a thymine modification found in various organism genomes. A novel enzyme-mediated bioorthogonal labeling method has been developed to selectively enrich 5hmU in genomes, allowing for a better understanding of its distribution and functional roles.
Article
Chemistry, Analytical
Qingyu Hu, Yuting Sun, Peihong Yuan, Hehua Lei, Huiqin Zhong, Yulan Wang, Huiru Tang
Summary: This study developed a method for detecting hydrophilic metabolites using ion-pair reversed-phase liquid chromatography coupled with mass spectrometry, which can quantify more than 260 metabolites simultaneously and is applicable for various biological samples, providing an efficient approach for large-scale quantitative hydrophilic metabolomic profiling.
Article
Biochemical Research Methods
R. Sanchez-Giraldo, F. J. Acosta-Reyes, C. S. Malarkey, N. Saperas, M. E. A. Churchill, J. L. Campos
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2015)
Article
Cell Biology
Christopher S. Malarkey, Claudia Lionetti, Stefania Deceglie, Marina Roberti, Mair E. A. Churchill, Palmiro Cantatore, Paola Loguercio Polosa
Article
Multidisciplinary Sciences
Henrick Horita, Christina L. Wysoczynski, Lori A. Walker, Karen S. Moulton, Marcella Li, Allison Ostriker, Rebecca Tucker, Timothy A. McKinsey, Mair E. A. Churchill, Raphael A. Nemenoff, Mary C. M. Weiser-Evans
NATURE COMMUNICATIONS
(2016)
Article
Biology
Wallace H. Liu, Sarah C. Roemer, Yeyun Zhou, Zih-Jie Shen, Briana K. Dennehey, Jeremy L. Balsbaugh, Jennifer C. Liddle, Travis Nemkov, Natalie G. Ahn, Kirk C. Hansen, Jessica K. Tyler, Mair E. A. Churchill
Article
Oncology
Jason E. Duex, Kalin E. Swain, Garrett M. Dancik, Richard D. Paucek, Charles Owens, Mair E. A. Churchill, Dan Theodorescu
MOLECULAR CANCER RESEARCH
(2018)
Correction
Biochemistry & Molecular Biology
Wallace H. Liu, Sarah C. Roemer, Alex M. Port, Mair E. A. Churchill
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Christina L. Wysoczynski-Horita, Michelle E. Boursier, Ryan Hill, Kirk Hansen, Helen E. Blackwell, Mair E. A. Churchill
MOLECULAR MICROBIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Paul V. Sauer, Yajie Gu, Wallace H. Liu, Francesca Mattiroli, Daniel Panne, Karolin Luger, Mair E. A. Churchill
NUCLEIC ACIDS RESEARCH
(2018)
Article
Multidisciplinary Sciences
Christopher S. Malarkey, Claire E. Gustafson, Jessica F. Saifee, Raul M. Torres, Mair E. A. Churchill, Edward N. Janoff
Article
Oncology
Sanja B. Turturro, Matthew S. Najor, Timothy Yung, Liam Portt, Christopher S. Malarkey, Abde M. Abukhdeir, Melody A. Cobleigh
BREAST CANCER RESEARCH AND TREATMENT
(2019)
Article
Biochemistry & Molecular Biology
Patrick H. Hewitt, Ernest D. Pianim, Nicholas A. DiCesare, Casey Gray, Trung T. Leong, Kuriko Sakai, Jan V. Bernal, Shweta S. Shetty, Christopher S. Malarkey
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2020)
Article
Biology
Ruben Rosas, Rhiannon R. Aguilar, Nina Arslanovic, Anna Seck, Duncan J. Smith, Jessica K. Tyler, Mair E. A. Churchill
Summary: The histone chaperone CAF-1 deposits histone H3/H4 dimers onto newly replicated DNA to form the central core of the nucleosome tetrasome. The KER SAH region of CAF-1 plays a crucial role in ensuring the assembly of tetrasomes by linking functional domains within CAF-1 with structural precision.
Article
Genetics & Heredity
Hannah Sleven, Seth J. Welsh, Jing Yu, Mair E. A. Churchill, Caroline F. Wright, Alex Henderson, Rita Horvath, Julia Rankin, Julie Vogt, Alex Magee, Vivienne McConnell, Andrew Green, Mary D. King, Helen Cox, Linlea Armstrong, Anna Lehman, Tanya N. Nelson, Jonathan Williams, Penny Clouston, James Hagman, Andrea H. Nemeth
AMERICAN JOURNAL OF HUMAN GENETICS
(2017)