Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region.

Abstract:

:Guanine-rich sequences are highly abundant in the human genome, especially in regulatory regions. Because guanine-rich sequences have the unique ability to form G-quadruplexes, these structures may play a role in the regulation of gene transcription. In previous studies, we demonstrated that formation of G-quadruplexes could be induced with peptide nucleic acids (PNAs). PNAs designed to bind the C-rich strand upstream of the human BCL2 gene promoted quadruplex formation in the complementary G-rich strand. However, the question whether G-quadruplex formation was essential for PNA invasion remained unanswered. In this study, we compared PNA invasion in the native and mutant, i.e. not forming G-quadruplex, BCL2 sequences and showed that G-quadruplex is required for effective PNA invasion into duplex DNA. This finding provides strong evidence for not only sequence-specific, but also quadruplex specific, gene targeting with PNA probes. In addition, we examined DNA-duplex invasion potential of PNAs of various charges. Using the gel shift assay, chemical probing and dimethyl sulfate (DMS) protection studies, we determined that uncharged zwitterionic PNA has the highest binding specificity while preserving efficient duplex invasion.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Onyshchenko MI,Gaynutdinov TI,Englund EA,Appella DH,Neumann RD,Panyutin IG

doi

10.1093/nar/gkr259

subject

Has Abstract

pub_date

2011-09-01 00:00:00

pages

7114-23

issue

16

eissn

0305-1048

issn

1362-4962

pii

gkr259

journal_volume

39

pub_type

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