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Conformational Diversity of Single-Stranded DNA from Bacterial Repetitive Extragenic Palindromes: Implications for the DNA Recognition Elements of Transposases

SYSNO ASEP	0450981
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Conformational Diversity of Single-Stranded DNA from Bacterial Repetitive Extragenic Palindromes: Implications for the DNA Recognition Elements of Transposases
Author(s)	Charnavets, Tatsiana (BTO-N) Nunvář, Jaroslav (BTO-N) Nečasová, Iva (BTO-N) Voelker, J. (US) Breslauer, K.J. (US) Schneider, Bohdan (BTO-N)_{RID, ORCID}
Source Title	Biopolymers - ISSN 0006-3525 Roč. 103, č. 10 (2015), s. 585-596
Number of pages	10 s.
Language	eng - English
Country	US - United States
Keywords	bacterial repetitive extragenic palindromes (REP) ; circular dichroism spectroscopy ; REP associated tyrosine transposases (RAYTs)
Subject RIV	EB - Genetics ; Molecular Biology
R&D Projects	ED1.1.00/02.0109 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	GAP305/12/1801 GA ČR - Czech Science Foundation (CSF)
	EE2.3.30.0020 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
Institutional support	BTO-N - RVO:86652036
UT WOS	000358620900005
DOI	10.1002/bip.22666
Annotation	Repetitive extragenic palindrome (REP)associated tyrosine transposase enzymes (RAYTs) bind REP DNA domains and catalyze their cleavage. Genomic sequence analyses identify potential noncoding REP sequences associated with RAYT-encoding genes. To probe the conformational space of potential RAYT DNA binding domains, we report here spectroscopic and calorimetric measurements that detect and partially characterize the solution conformational heterogeneity of REP oligonucleotides from six bacterial species. Our data reveal most of these REP oligonucleotides adopt multiple conformations, suggesting that RAYTs confront a landscape of potential DNA substrates in dynamic equilibrium that could be selected, enriched, and/or induced via differential binding. Thus, the transposase-bound DNA motif may not be the predominant conformation of the isolated REP domain. Intriguingly, for several REPs, the circular dichroism spectra suggest guanine tetraplexes as potential alternative or additional RAYT recognition elements, an observation consistent with these REP domains being highly nonrandom, with tetraplex-favoring 5-G and 3-C-rich segments. In fact, the conformational heterogeneity of REP domains detected and reported here, including the formation of noncanonical DNA secondary structures, may reflect a general feature required for recognition by RAYT transposases. Based on our biophysical data, we propose guanine tetraplexes as an additional DNA recognition element for binding by RAYT transposase enzymes
Workplace	Institute of Biotechnology
Contact	Monika Kopřivová, Monika.Koprivova@ibt.cas.cz, Tel.: 325 873 700
Year of Publishing	2016

Number of the records: 1