Screening Natural and Modified Nucleobases to Create Alkylation-Resistant Nucleic Acids Toward Sensing Applications
- 1Department of Chemistry
- 2Washington University in St. Louis
Abstract
Alkylating agents play critical roles in medicine and chemical defense but also pose significant hazards by modifying DNA and disrupting cellular function. Their reliable detection is therefore critical, yet current analytical methods are often limited by poor selectivity, need for extensive sample preparation, or poor compatibility with complex matrices. Nucleic acid sensors, such as aptamers, offer a promising route to achieve selective sensing. However, alkylation of nucleobases can compromise DNA three-dimensional structure and binding abilities. To address this limitation, we sought to develop DNA sequences that are resistant to alkylation. We first evaluated the reactivity of modified nucleobases toward a panel of alkylating agents. Although the N7 position 2 of guanosine and N3 position of adenosine have been reported to be among the primary alkylation sites, their analogues 7-deaza-2′-deoxyguanosine and 3-deaza-2′-deoxyadensoine were still found to be reactive. In contrast, 7-deaza-2′-deoxyinosine and 7-deaza-2′-deoxyadenosine were resistant to all alkylating agents tested. Using these resistant nucleobases as substitutes for all guanosine and adenosine residues, respectively, we screened polymerases and found that Therminator DNA Polymerase enabled enzymatic synthesis of fully alkylation-resistant DNA. This work establishes a chemical framework for the development of robust, DNA-based sensors for alkylating agents in biomedical and defense applications.
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BibTeX
@misc{ibukun2026screening,
title = {{Screening Natural and Modified Nucleobases to Create Alkylation-Resistant Nucleic Acids Toward Sensing Applications}},
author = {Olamilekan Joseph Ibukun and Makenzie R. Walk and Jennifer M. Heemstra},
howpublished = {ChemRxiv},
year = {2026},
month = sep,
doi = {10.26434/chemrxiv.15008995/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008995/v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Screening Natural and Modified Nucleobases to Create Alkylation-Resistant Nucleic Acids Toward Sensing Applications
AU - Olamilekan Joseph Ibukun
AU - Makenzie R. Walk
AU - Jennifer M. Heemstra
PY - 2026
DA - 2026/09/17
PB - ChemRxiv
DO - 10.26434/chemrxiv.15008995/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008995/v1
AB - Alkylating agents play critical roles in medicine and chemical defense but also pose significant hazards by modifying DNA and disrupting cellular function. Their reliable detection is therefore critical, yet current analytical methods are often limited by poor selectivity, need for extensive sample preparation, or poor compatibility with complex matrices. Nucleic acid sensors, such as aptamers, offer a promising route to achieve selective sensing. However, alkylation of nucleobases can compromise DNA three-dimensional structure and binding abilities. To address this limitation, we sought to develop DNA sequences that are resistant to alkylation. We first evaluated the reactivity of modified nucleobases toward a panel of alkylating agents. Although the N7 position 2 of guanosine and N3 position of adenosine have been reported to be among the primary alkylation sites, their analogues 7-deaza-2′-deoxyguanosine and 3-deaza-2′-deoxyadensoine were still found to be reactive. In contrast, 7-deaza-2′-deoxyinosine and 7-deaza-2′-deoxyadenosine were resistant to all alkylating agents tested. Using these resistant nucleobases as substitutes for all guanosine and adenosine residues, respectively, we screened polymerases and found that Therminator DNA Polymerase enabled enzymatic synthesis of fully alkylation-resistant DNA. This work establishes a chemical framework for the development of robust, DNA-based sensors for alkylating agents in biomedical and defense applications.
ER -