Enhancing the Interactions of Ion-Tagged Oligonucleotides and Magnetic Ionic Liquid Supports for the Sequence-Specific Extraction of Hepatitis B Virus DNA
Seong-Soo Lee, Derek R. Eitzmann, Jared L. Anderson
{"title":"Enhancing the Interactions of Ion-Tagged Oligonucleotides and Magnetic Ionic Liquid Supports for the Sequence-Specific Extraction of Hepatitis B Virus DNA","authors":"Seong-Soo Lee, Derek R. Eitzmann, Jared L. Anderson","doi":"10.1016/j.aca.2024.343563","DOIUrl":null,"url":null,"abstract":"<h3>Background</h3>Infections from the hepatitis B virus (HBV) are a major risk factor for hepatocellular carcinoma, one of the most common types of liver cancer. Circulating cell-free DNA (ccfDNA) in human plasma can be used as a non-invasive biomarker for diagnosing HBV-related liver diseases. The isolation of target ccfDNA sequences is often challenging due to the co-extraction of highly abundant non-target DNA from samples. Ion-tagged oligonucleotide (ITO) probes coupled with magnetic ionic liquids (MIL) support have emerged as a promising methodology for sequence-specific DNA extractions to address challenges associated with solid supports such as streptavidin-coated magnetic bead.<h3>Results</h3>ITOs, disubstituted ion-tagged oligonucleotide (DTO), and ion-tagged disubstituted oligonucleotide (ITDO) probes featuring various substituents including linear alkyl, branched alkyl, and perfluoroalkyl moieties were examined to enhance hydrophobic and fluorophilic interactions between the probes and a trihexyl(tetradecyl)phosphonium manganese(II) hexafluoroacetylacetonate ([P<sub>66614</sub><sup>+</sup>][Mn(hfacac)<sub>3</sub><sup>−</sup>]) MIL support. The ITO-MIL approach was optimized by adjusting the annealing temperature (45 °C), molar ratio of target DNA to ITO probe (1:100), and ionic strength (200 mM NaCl) to maximize the extraction of target DNA. The 3-allyl-1-(23-bis(pentylthio)propyl)imidazolium bromide ([AI(C<sub>5</sub>S)<sub>2</sub><sup>+</sup>][Br<sup>-</sup>])-ITO probe featuring a branched alkyl substituent yielded a higher loading efficiency (48.05 ± 6.72%) due to increased hydrophobic ITO-MIL interactions, compared to that of 24.57 ± 4.40% for the 3-allyl-1-(3-(pentylthio)propyl)imidazolium bromide ([AIC<sub>5</sub>S<sup>+</sup>][Br<sup>-</sup>])-ITO probe with a linear alkyl substituent. The high affinity of ITO-MILinteractions minimized the loss of probe during successive wash steps, yielding an approximate 10-fold greater amount of extracted target DNA using the [AI(C<sub>5</sub>S)<sub>2</sub><sup>+</sup>][Br<sup>-</sup>])-ITO probe compared to [AIC<sub>5</sub>S<sup>+</sup>][Br<sup>-</sup>])-ITO probe.<h3>Significance</h3>This study provides novel synthetic approaches for tailoring probe substituents using thiol-ene and thiol-yne “click” chemistry. Hydrophobic and fluorophilic ITO-MIL interactions were systematically investigated. Optimal conditions for the ITO-MIL method significantly improved the amount of extracted DNA. The ITO-MIL method using the [AI(C<sub>5</sub>S)<sub>2</sub><sup>+</sup>][Br<sup>-</sup>]-HBV-ITO probe demonstrated selective extraction of target HBV DNA in both DI water and diluted human plasma containing a high abundance of background DNA.","PeriodicalId":240,"journal":{"name":"Analytica Chimica Acta","volume":"106 1","pages":""},"PeriodicalIF":5.7000,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Analytica Chimica Acta","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1016/j.aca.2024.343563","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, ANALYTICAL","Score":null,"Total":0}
引用次数: 0
Abstract
Background
Infections from the hepatitis B virus (HBV) are a major risk factor for hepatocellular carcinoma, one of the most common types of liver cancer. Circulating cell-free DNA (ccfDNA) in human plasma can be used as a non-invasive biomarker for diagnosing HBV-related liver diseases. The isolation of target ccfDNA sequences is often challenging due to the co-extraction of highly abundant non-target DNA from samples. Ion-tagged oligonucleotide (ITO) probes coupled with magnetic ionic liquids (MIL) support have emerged as a promising methodology for sequence-specific DNA extractions to address challenges associated with solid supports such as streptavidin-coated magnetic bead.
Results
ITOs, disubstituted ion-tagged oligonucleotide (DTO), and ion-tagged disubstituted oligonucleotide (ITDO) probes featuring various substituents including linear alkyl, branched alkyl, and perfluoroalkyl moieties were examined to enhance hydrophobic and fluorophilic interactions between the probes and a trihexyl(tetradecyl)phosphonium manganese(II) hexafluoroacetylacetonate ([P66614+][Mn(hfacac)3−]) MIL support. The ITO-MIL approach was optimized by adjusting the annealing temperature (45 °C), molar ratio of target DNA to ITO probe (1:100), and ionic strength (200 mM NaCl) to maximize the extraction of target DNA. The 3-allyl-1-(23-bis(pentylthio)propyl)imidazolium bromide ([AI(C5S)2+][Br-])-ITO probe featuring a branched alkyl substituent yielded a higher loading efficiency (48.05 ± 6.72%) due to increased hydrophobic ITO-MIL interactions, compared to that of 24.57 ± 4.40% for the 3-allyl-1-(3-(pentylthio)propyl)imidazolium bromide ([AIC5S+][Br-])-ITO probe with a linear alkyl substituent. The high affinity of ITO-MILinteractions minimized the loss of probe during successive wash steps, yielding an approximate 10-fold greater amount of extracted target DNA using the [AI(C5S)2+][Br-])-ITO probe compared to [AIC5S+][Br-])-ITO probe.
Significance
This study provides novel synthetic approaches for tailoring probe substituents using thiol-ene and thiol-yne “click” chemistry. Hydrophobic and fluorophilic ITO-MIL interactions were systematically investigated. Optimal conditions for the ITO-MIL method significantly improved the amount of extracted DNA. The ITO-MIL method using the [AI(C5S)2+][Br-]-HBV-ITO probe demonstrated selective extraction of target HBV DNA in both DI water and diluted human plasma containing a high abundance of background DNA.
期刊介绍:
Analytica Chimica Acta has an open access mirror journal Analytica Chimica Acta: X, sharing the same aims and scope, editorial team, submission system and rigorous peer review.
Analytica Chimica Acta provides a forum for the rapid publication of original research, and critical, comprehensive reviews dealing with all aspects of fundamental and applied modern analytical chemistry. The journal welcomes the submission of research papers which report studies concerning the development of new and significant analytical methodologies. In determining the suitability of submitted articles for publication, particular scrutiny will be placed on the degree of novelty and impact of the research and the extent to which it adds to the existing body of knowledge in analytical chemistry.