Synthesis and properties of cross-linkable DNA duplex using 4-amino-2-oxo-6-vinyl-1,3,5-triazine

Ken Yamada; Shogo Ishiyama; Kazumitsu Onizuka; Fumi Nagatsugi

doi:10.1016/j.tet.2017.01.043

Synthesis and properties of cross-linkable DNA duplex using 4-amino-2-oxo-6-vinyl-1,3,5-triazine

Ken Yamada, Shogo Ishiyama, Kazumitsu Onizuka, Fumi Nagatsugi

Division of Organic- and Biomaterials Research

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Abstract

We synthesized the DNA oligonucleotide containing a new cross-linkable 4-amino-2-oxo-6-vinyltriazine (AOVT) nucleobase analogue (Et-AOVT) and evaluated these properties. Our results of the cross-link assay and thermal denaturing assay of duplexes containing AOVT demonstrated that the additional aza of AOVT has an impact on the duplex stability and crosslink properties. Our data suggests that the additional 5-aza of AOVT is involved in the hydrogen bonding with the complementary guanine, and this hydrogen bonding system successfully flipped the reactive vinyl group out to the major groove of the duplex demonstrating a new paradigm of a “cross-linkable duplex”.

Original language	English
Pages (from-to)	1424-1435
Number of pages	12
Journal	Tetrahedron
Volume	73
Issue number	11
DOIs	https://doi.org/10.1016/j.tet.2017.01.043
Publication status	Published - 2017

Keywords

Crosslink
Nucleic acid binding proteins
Oligonucleotides
Vinyl triazine

ASJC Scopus subject areas

Biochemistry
Drug Discovery
Organic Chemistry

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10.1016/j.tet.2017.01.043

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title = "Synthesis and properties of cross-linkable DNA duplex using 4-amino-2-oxo-6-vinyl-1,3,5-triazine",

abstract = "We synthesized the DNA oligonucleotide containing a new cross-linkable 4-amino-2-oxo-6-vinyltriazine (AOVT) nucleobase analogue (Et-AOVT) and evaluated these properties. Our results of the cross-link assay and thermal denaturing assay of duplexes containing AOVT demonstrated that the additional aza of AOVT has an impact on the duplex stability and crosslink properties. Our data suggests that the additional 5-aza of AOVT is involved in the hydrogen bonding with the complementary guanine, and this hydrogen bonding system successfully flipped the reactive vinyl group out to the major groove of the duplex demonstrating a new paradigm of a “cross-linkable duplex”.",

keywords = "Crosslink, Nucleic acid binding proteins, Oligonucleotides, Vinyl triazine",

author = "Ken Yamada and Shogo Ishiyama and Kazumitsu Onizuka and Fumi Nagatsugi",

note = "Funding Information: This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas (“Middle Molecular Strategy.” JP15H05838) and a Grant-in-Aid for Scientific Research (B) (25288073) from the Japan Society for the Promotion of Science. This work was also supported in part by the Management Expenses Grants National Universities Corporations from the Ministry of Education, Science, Sports and Culture of Japan (MEXT). Publisher Copyright: {\textcopyright} 2017",

year = "2017",

doi = "10.1016/j.tet.2017.01.043",

language = "English",

volume = "73",

pages = "1424--1435",

journal = "Tetrahedron",

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publisher = "Elsevier Limited",

number = "11",

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TY - JOUR

T1 - Synthesis and properties of cross-linkable DNA duplex using 4-amino-2-oxo-6-vinyl-1,3,5-triazine

AU - Yamada, Ken

AU - Ishiyama, Shogo

AU - Onizuka, Kazumitsu

AU - Nagatsugi, Fumi

N1 - Funding Information: This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas (“Middle Molecular Strategy.” JP15H05838) and a Grant-in-Aid for Scientific Research (B) (25288073) from the Japan Society for the Promotion of Science. This work was also supported in part by the Management Expenses Grants National Universities Corporations from the Ministry of Education, Science, Sports and Culture of Japan (MEXT). Publisher Copyright: © 2017

PY - 2017

Y1 - 2017

N2 - We synthesized the DNA oligonucleotide containing a new cross-linkable 4-amino-2-oxo-6-vinyltriazine (AOVT) nucleobase analogue (Et-AOVT) and evaluated these properties. Our results of the cross-link assay and thermal denaturing assay of duplexes containing AOVT demonstrated that the additional aza of AOVT has an impact on the duplex stability and crosslink properties. Our data suggests that the additional 5-aza of AOVT is involved in the hydrogen bonding with the complementary guanine, and this hydrogen bonding system successfully flipped the reactive vinyl group out to the major groove of the duplex demonstrating a new paradigm of a “cross-linkable duplex”.

AB - We synthesized the DNA oligonucleotide containing a new cross-linkable 4-amino-2-oxo-6-vinyltriazine (AOVT) nucleobase analogue (Et-AOVT) and evaluated these properties. Our results of the cross-link assay and thermal denaturing assay of duplexes containing AOVT demonstrated that the additional aza of AOVT has an impact on the duplex stability and crosslink properties. Our data suggests that the additional 5-aza of AOVT is involved in the hydrogen bonding with the complementary guanine, and this hydrogen bonding system successfully flipped the reactive vinyl group out to the major groove of the duplex demonstrating a new paradigm of a “cross-linkable duplex”.

KW - Crosslink

KW - Nucleic acid binding proteins

KW - Oligonucleotides

KW - Vinyl triazine

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U2 - 10.1016/j.tet.2017.01.043

DO - 10.1016/j.tet.2017.01.043

M3 - Article

AN - SCOPUS:85011305584

SN - 0040-4020

VL - 73

SP - 1424

EP - 1435

JO - Tetrahedron

JF - Tetrahedron

IS - 11

ER -

Synthesis and properties of cross-linkable DNA duplex using 4-amino-2-oxo-6-vinyl-1,3,5-triazine

Abstract

Keywords

ASJC Scopus subject areas

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