Recognition of 5-methyl-CG and CG base pairs in duplex DNA with high stability using antiparallel-type triplex-forming oligonucleotides with 2-guanidinoethyl-2'-deoxynebularine.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
28 11 2022
28 11 2022
Historique:
accepted:
05
11
2022
revised:
26
10
2022
received:
08
07
2022
pubmed:
2
12
2022
medline:
21
12
2022
entrez:
1
12
2022
Statut:
ppublish
Résumé
The formation of triplex DNA is a site-specific recognition method that directly targets duplex DNA. However, triplex DNA formation is generally formed for the GC and AT base pairs of duplex DNA, and there are no natural nucleotides that recognize the CG and TA base pairs, or even the 5-methyl-CG (5mCG) base pair. Moreover, duplex DNA, including 5mCG base pairs, epigenetically regulates gene expression in vivo, and thus targeting strategies are of biological importance. Therefore, the development of triplex-forming oligonucleotides (TFOs) with artificial nucleosides that selectively recognize these base pairs with high affinity is needed. We recently reported that 2'-deoxy-2-aminonebularine derivatives exhibited the ability to recognize 5mCG and CG base pairs in triplex formation; however, this ability was dependent on sequences. Therefore, we designed and synthesized new nucleoside derivatives based on the 2'-deoxy-nebularine (dN) skeleton to shorten the linker length connecting to the hydrogen-bonding unit in formation of the antiparallel motif triplex. We successfully demonstrated that TFOs with 2-guanidinoethyl-2'-deoxynebularine (guanidino-dN) recognized 5mCG and CG base pairs with very high affinity in all four DNA sequences with different adjacent nucleobases of guanidino-dN as well as in the promoter sequences of human genes containing 5mCG base pairs with a high DNA methylation frequency.
Identifiants
pubmed: 36454012
pii: 6858762
doi: 10.1093/nar/gkac1110
pmc: PMC9757063
doi:
Substances chimiques
Oligonucleotides
0
2'-deoxynebularine
4546-68-3
DNA
9007-49-2
Deoxyribonucleosides
0
Nucleosides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
12071-12081Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6870-5
pubmed: 9618505
Hum Mol Genet. 2007 Apr 15;16 Spec No 1:R50-9
pubmed: 17613547
Biochemistry. 2005 Dec 20;44(50):16695-700
pubmed: 16342959
Biochimie. 2008 Aug;90(8):1117-30
pubmed: 18331847
J Org Chem. 2016 Nov 18;81(22):11000-11008
pubmed: 27779877
Cell. 1983 May;33(1):9-10
pubmed: 6205762
Org Biomol Chem. 2012 Oct 3;10(41):8336-41
pubmed: 22987068
Nucleic Acids Res. 2018 Feb 16;46(3):1021-1037
pubmed: 29228337
Annu Rev Biochem. 1995;64:65-95
pubmed: 7574496
J Mol Biol. 1997 Jul 18;270(3):385-95
pubmed: 9237905
Org Biomol Chem. 2014 Nov 28;12(44):9011-5
pubmed: 25285418
Biochemistry. 1991 Nov 19;30(46):11018-25
pubmed: 1932026
Science. 1992 Nov 27;258(5087):1463-6
pubmed: 1279808
Nucleic Acids Res. 2018 Sep 28;46(17):8679-8688
pubmed: 30102410
Epigenomics. 2009 Oct;1(1):177-200
pubmed: 22122642
Psychiatry Res. 2018 Jul;265:341-348
pubmed: 29793048
Nucleic Acids Res. 1982 Apr 24;10(8):2709-21
pubmed: 7079182
Nature. 1989 Jun 22;339(6226):637-40
pubmed: 2733796
Nature. 1986 May 15-21;321(6067):209-13
pubmed: 2423876
J Mol Biol. 1994 Jul 1;240(1):42-51
pubmed: 8021939
Curr Med Chem. 2000 Jan;7(1):17-37
pubmed: 10637355
Biochim Biophys Acta. 1999 Dec 10;1489(1):181-206
pubmed: 10807007
Org Biomol Chem. 2020 Apr 15;18(15):2845-2851
pubmed: 32232234
J Clin Invest. 2003 Aug;112(4):487-94
pubmed: 12925687
J Phys Chem A. 2010 May 13;114(18):5932-9
pubmed: 20402487
J Biol Chem. 2003 Feb 7;278(6):4035-40
pubmed: 12427740
Nucleic Acids Res. 2021 Aug 20;49(14):e81
pubmed: 34019650
J Natl Cancer Inst. 2001 May 2;93(9):691-9
pubmed: 11333291
RSC Adv. 2021 Jun 16;11(35):21390-21396
pubmed: 35478801
Org Biomol Chem. 2013 Jun 21;11(23):3918-24
pubmed: 23660599
Mol Cell Biol. 1998 Nov;18(11):6538-47
pubmed: 9774669
Epigenetics. 2019 Dec;14(12):1141-1163
pubmed: 31284823
Angew Chem Int Ed Engl. 2017 Nov 27;56(48):15210-15233
pubmed: 28444822
Bioorg Med Chem. 2020 Apr 1;28(7):115350
pubmed: 32115336
ACS Biomater Sci Eng. 2022 May 9;8(5):1799-1805
pubmed: 35263539
Angew Chem Int Ed Engl. 2016 Sep 26;55(40):12445-9
pubmed: 27576703
Mol Cell Biol. 1994 Aug;14(8):5487-94
pubmed: 7518564
Cell. 1990 Aug 10;62(3):503-14
pubmed: 1974172
Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7504-9
pubmed: 11390984
Science. 2011 Sep 2;333(6047):1300-3
pubmed: 21778364