A diastereomeric mixture of the regioisomers O6-(2-hydroxy-2-phenylethyl)-2'-deoxyguanosine (st6G, beta-isomer) and O6-(2-hydroxy-1-phenylethyl)-2'-deoxyguanosine (alpha-isomer) was site-specifically placed in a 25 base oligonucleotide template 5'-CCGCTAst6GCGGGTACCGAGCTCGAAT-3' using CED phosphoramidite chemistry. Using 32P-post-labeling we found the oligonucleotide to contain 95% of the beta-isomer and 5% of the alpha-isomer of st6G. st6G as the 3'-phosphate was found to be considerably more acid labile than O6-methyl-2'-deoxyguanosine-3'-phosphate, leading to dealkylation during oligonucleotide synthesis. The diastereomeric mixture of O6-(2-hydroxy-2-phenylethyl)-2'-deoxy-guanosine-5'-triphosphate (st6dGTP) was chemically synthesized and used as a substrate for the exonuclease-free Klenow fragment of Escherichia coli DNA polymerase I. This study demonstrated that st6dGTP could be incorporated opposite deoxycytidine and did not completely block replication.
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http://dx.doi.org/10.1093/carcin/15.7.1371 | DOI Listing |
J Pharm Sci
January 2025
Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010. Electronic address:
Complexes formed between aluminum cluster molecules that adopt a Ɛ-Al-Keggin structure and antisense oligonucleotides were observed as new impurity peaks during drug product stability testing. The Ɛ-Al-Keggin molecules were determined to be artifacts of the analysis, originating from contact between antisense oligonucleotide drug product solution and aluminum weigh boats used to prepare the analytical sample solutions The presence of the Ɛ-Al-Keggin molecules was confirmed through synthesis of the Keggin molecule through an established route and subsequent spiking studies. Binding affinity studies revealed that the Ɛ-Al-Keggin bound to oligonucleotide sequences of various lengths (10 to 20 bases) and base compositions, though there is some evidence for preferential binding to 5-methylcytosine-containing sequences.
View Article and Find Full Text PDFMol Ther Nucleic Acids
March 2025
Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan.
Currently, no drugs directly treat liver fibrosis. Previously, we have shown that treatment with miR-29a-3p improved liver fibrosis in a mouse model. To investigate the effectiveness of nucleic acid therapy at a lower dose, a modified nucleic acid was prepared based on miR-29a-3p.
View Article and Find Full Text PDFEpilepsia
January 2025
Atalanta Therapeutics, Boston, Massachusetts, USA.
Objective: Gain-of-function variants in the KCNT1 gene, which encodes a sodium-activated potassium ion channel, drive severe early onset developmental epileptic encephalopathies including epilepsy of infancy with migrating focal seizures and sleep-related hypermotor epilepsy. No therapy provides more than sporadic or incremental improvement. Here, we report suppression of seizures in a genetic mouse model of KCNT1 epilepsy by reducing Kcnt1 transcript with divalent small interfering RNA (siRNA), an emerging variant of oligonucleotide technology developed for the central nervous system.
View Article and Find Full Text PDFMicromachines (Basel)
January 2025
State Key Laboratory of Radio Frequency Heterogeneous Integration, Shanghai Jiao Tong University, Shanghai 200240, China.
On-chip gene synthesis has the potential to improve the synthesis throughput and reduce the cost exponentially. While there exist several microarray-based oligo synthesis technologies, on-chip gene assembly has yet to be demonstrated. This work introduces a novel on-chip DNA assembly method via dielectrophoresis (DEP) that can potentially be integrated with microarray-based oligo synthesis on the same chip.
View Article and Find Full Text PDFMikrochim Acta
January 2025
Key Laboratory for Palygorskite Science and Applied Technology of Jiangsu Province, National & Local Joint Engineering Research Center for Mineral Salt Deep Utilization, Huaiyin Institute of Technology, Huaian, 223003, P. R. China.
A highly sensitive and selective electrochemical biosensor was developed for the detection of kanamycin using a core-hollow-shell structured peroxidase-mimic nanozyme, CHS-Fe₃O₄@@ZIF-8. The synthesized CHS-FeO@@ZIF-8 was characterized with scanning electron microscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy. It was found that the CHS-FeO@@ZIF-8 exhibits excellent peroxidase-like activity due to its ultra-thin hollow layer.
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