{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Wang X"],"funding":["Welch Foundation","Japan Science and Technology Agency","National Institute of General Medical Sciences","NIGMS NIH HHS"],"pagination":["1748-1752"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10926321"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["146(3)"],"pubmed_abstract":["Single-stranded DNA (ssDNA) oligonucleotides are widely used in biological research, therapeutics, biotechnology, and nanomachines. Large-scale enzymatic production of ssDNA oligonucleotides forming noncanonical structures has been difficult. Here, we present a simple and robust method named \"palindrome-nicking-dependent amplification\" (PaNDA) for enzymatic production of a large amount of ssDNA oligonucleotides. It utilizes a strand-displacing DNA polymerase and a nicking enzyme together with input DNA and deoxynucleotide triphosphates at 55 °C. Scaling up of PaNDA is straightforward due to its isothermal nature. The ssDNA products can easily be isolated through anion-exchange chromatography under nondenaturing conditions. We demonstrate applications of PaNDA to <sup>13</sup>C/<sup>15</sup>N-labeling of various DNA strands, including a 22-nt telomere repeat G-quadruplex, a 26-nt therapeutic aptamer, and a 33-nt DNAzyme. The <sup>13</sup>C/<sup>15</sup>N-labeling by PaNDA greatly facilitates the characterization of noncanonical DNA by nuclear magnetic resonance (NMR) spectroscopy. For example, the behavior of therapeutic DNA aptamers in human serum can be investigated."],"journal":["Journal of the American Chemical Society"],"pubmed_title":["Robust Enzymatic Production of DNA G-Quadruplex, Aptamer, DNAzyme, and Other Oligonucleotides: Applications for NMR."],"pmcid":["PMC10926321"],"funding_grant_id":["R35-GM130326","JPMJFS2125","R35 GM130326","H-2104-20220331"],"pubmed_authors":["Paz-Villatoro JM","Yu B","Iwahara J","Sakurabayashi S","Wang X"],"additional_accession":[]},"is_claimable":false,"name":"Robust Enzymatic Production of DNA G-Quadruplex, Aptamer, DNAzyme, and Other Oligonucleotides: Applications for NMR.","description":"Single-stranded DNA (ssDNA) oligonucleotides are widely used in biological research, therapeutics, biotechnology, and nanomachines. Large-scale enzymatic production of ssDNA oligonucleotides forming noncanonical structures has been difficult. Here, we present a simple and robust method named \"palindrome-nicking-dependent amplification\" (PaNDA) for enzymatic production of a large amount of ssDNA oligonucleotides. It utilizes a strand-displacing DNA polymerase and a nicking enzyme together with input DNA and deoxynucleotide triphosphates at 55 °C. Scaling up of PaNDA is straightforward due to its isothermal nature. The ssDNA products can easily be isolated through anion-exchange chromatography under nondenaturing conditions. We demonstrate applications of PaNDA to <sup>13</sup>C/<sup>15</sup>N-labeling of various DNA strands, including a 22-nt telomere repeat G-quadruplex, a 26-nt therapeutic aptamer, and a 33-nt DNAzyme. The <sup>13</sup>C/<sup>15</sup>N-labeling by PaNDA greatly facilitates the characterization of noncanonical DNA by nuclear magnetic resonance (NMR) spectroscopy. For example, the behavior of therapeutic DNA aptamers in human serum can be investigated.","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Jan","modification":"2025-04-03T23:36:16.939Z","creation":"2025-04-03T23:36:16.939Z"},"accession":"S-EPMC10926321","cross_references":{"pubmed":["38191993"],"doi":["10.1021/jacs.3c11219"]}}