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Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides

Oxanine (Oxa, O), one of the major damaged bases from guanine generated by NO- or HNO(2)-induced nitrosative deamination, has been considered as a mutagen-potent lesion. For exploring more detailed properties of Oxa, large-scale preparation of Oxa-containing oligodeoxynucleotide (Oxa-ODN) with the d...

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Autores principales: Pack, Seung Pil, Nonogawa, Mitsuru, Kodaki, Tsutomu, Makino, Keisuke
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1255731/
https://www.ncbi.nlm.nih.gov/pubmed/16219806
http://dx.doi.org/10.1093/nar/gki865
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author Pack, Seung Pil
Nonogawa, Mitsuru
Kodaki, Tsutomu
Makino, Keisuke
author_facet Pack, Seung Pil
Nonogawa, Mitsuru
Kodaki, Tsutomu
Makino, Keisuke
author_sort Pack, Seung Pil
collection PubMed
description Oxanine (Oxa, O), one of the major damaged bases from guanine generated by NO- or HNO(2)-induced nitrosative deamination, has been considered as a mutagen-potent lesion. For exploring more detailed properties of Oxa, large-scale preparation of Oxa-containing oligodeoxynucleotide (Oxa-ODN) with the desired base sequence is a prerequisite. In the present study, we have developed a chemical synthesis procedure of Oxa-ODNs and characterized thermodynamic properties of Oxa in DNA strands. First, 2′-deoxynucleoside of Oxa (dOxo) obtained from 2′-deoxyguanosine by HNO(2)-nitrosation was subjected to 5′-O-selective tritylation to give 5′-O-(4,4′-dimethoxytrityl)-dOxo (DMT-dOxo) with a maximum yield of 70%. Subsequently, DMT-dOxo was treated with conventional phosphoramidation, which resulted in DMT-dOxo-amidite monomer with a maximum yield of 72.5%. The amidite obtained was used for synthesizing Oxa-ODNs: the coupling yields for Oxa incorporation were over 93%. The prepared Oxa-ODNs were employed for analyzing the thermodynamic properties of DNA duplexes containing base-matches of O:N [N; C (cytosine), T (thymine), G (guanine) or A (adenine)]. Melting temperatures (T(m)) and thermodynamic stability ([Formula: see text]) were found to be lower by 6.83∼13.41°C and 2.643∼6.047 kcal mol(−1), respectively, compared with those of oligodeoxynucleotides, which had the same base sequence except that O:N was replaced by G:C (wild type). It has also been found that Oxa-pairing with cytosine shows relatively high stability in DNA duplex compared with other base combinations. The orders of [Formula: see text] were O:C > O:T > O:A > O:G. The chemical synthesis procedure and thermodynamic characteristics of Oxa-ODNs established here will be helpful for elucidating the biological significance of Oxa in relation to genotoxic and repair mechanisms.
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spelling pubmed-12557312005-10-24 Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides Pack, Seung Pil Nonogawa, Mitsuru Kodaki, Tsutomu Makino, Keisuke Nucleic Acids Res Article Oxanine (Oxa, O), one of the major damaged bases from guanine generated by NO- or HNO(2)-induced nitrosative deamination, has been considered as a mutagen-potent lesion. For exploring more detailed properties of Oxa, large-scale preparation of Oxa-containing oligodeoxynucleotide (Oxa-ODN) with the desired base sequence is a prerequisite. In the present study, we have developed a chemical synthesis procedure of Oxa-ODNs and characterized thermodynamic properties of Oxa in DNA strands. First, 2′-deoxynucleoside of Oxa (dOxo) obtained from 2′-deoxyguanosine by HNO(2)-nitrosation was subjected to 5′-O-selective tritylation to give 5′-O-(4,4′-dimethoxytrityl)-dOxo (DMT-dOxo) with a maximum yield of 70%. Subsequently, DMT-dOxo was treated with conventional phosphoramidation, which resulted in DMT-dOxo-amidite monomer with a maximum yield of 72.5%. The amidite obtained was used for synthesizing Oxa-ODNs: the coupling yields for Oxa incorporation were over 93%. The prepared Oxa-ODNs were employed for analyzing the thermodynamic properties of DNA duplexes containing base-matches of O:N [N; C (cytosine), T (thymine), G (guanine) or A (adenine)]. Melting temperatures (T(m)) and thermodynamic stability ([Formula: see text]) were found to be lower by 6.83∼13.41°C and 2.643∼6.047 kcal mol(−1), respectively, compared with those of oligodeoxynucleotides, which had the same base sequence except that O:N was replaced by G:C (wild type). It has also been found that Oxa-pairing with cytosine shows relatively high stability in DNA duplex compared with other base combinations. The orders of [Formula: see text] were O:C > O:T > O:A > O:G. The chemical synthesis procedure and thermodynamic characteristics of Oxa-ODNs established here will be helpful for elucidating the biological significance of Oxa in relation to genotoxic and repair mechanisms. Oxford University Press 2005 2005-10-11 /pmc/articles/PMC1255731/ /pubmed/16219806 http://dx.doi.org/10.1093/nar/gki865 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Article
Pack, Seung Pil
Nonogawa, Mitsuru
Kodaki, Tsutomu
Makino, Keisuke
Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides
title Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides
title_full Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides
title_fullStr Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides
title_full_unstemmed Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides
title_short Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides
title_sort chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1255731/
https://www.ncbi.nlm.nih.gov/pubmed/16219806
http://dx.doi.org/10.1093/nar/gki865
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