A fluorescent 3,7-bis-(naphthalen-1-ylethynylated)-2′-deoxyadenosine analogue reports thymidine in complementary DNA by a large emission Stokes shift

2018 ◽  
Vol 16 (9) ◽  
pp. 1496-1507 ◽  
Author(s):  
Masaki Yanagi ◽  
Azusa Suzuki ◽  
Robert H. E. Hudson ◽  
Yoshio Saito
Keyword(s):  
Stokes Shift ◽  
Minor Groove ◽  
Base Pairing ◽  
Complementary Dna ◽  
Adenosine Analogue

The first example of a fluorescent adenosine analogue possessing simultaneous major- and minor-groove substitution selectively reports base-pairing to thymidine.

scholarly journals Mutagenesis mechanism of the major oxidative adenine lesion 7,8-dihydro-8-oxoadenine

2020 ◽  
Vol 48 (9) ◽  
pp. 5119-5134 ◽  
Author(s):  
Myong-Chul Koag ◽  
Hunmin Jung ◽  
Seongmin Lee
Keyword(s):  
Reactive Oxygen Species ◽  
Crystal Structures ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Reactive Oxygen ◽  
Minor Groove ◽  
Oxygen Species ◽  
Base Pairing ◽  
Human Dna ◽  
Hoogsteen Base Pairing

Abstract Reactive oxygen species generate the genotoxic 8-oxoguanine (oxoG) and 8-oxoadenine (oxoA) as major oxidative lesions. The mutagenicity of oxoG is attributed to the lesion's ability to evade the geometric discrimination of DNA polymerases by adopting Hoogsteen base pairing with adenine in a Watson–Crick-like geometry. Compared with oxoG, the mutagenesis mechanism of oxoA, which preferentially induces A-to-C mutations, is poorly understood. In the absence of protein contacts, oxoA:G forms a wobble conformation, the formation of which is suppressed in the catalytic site of most DNA polymerases. Interestingly, human DNA polymerase η (polη) proficiently incorporates dGTP opposite oxoA, suggesting the nascent oxoA:dGTP overcomes the geometric discrimination of polη. To gain insights into oxoA-mediated mutagenesis, we determined crystal structures of polη bypassing oxoA. When paired with dGTP, oxoA adopted a syn-conformation and formed Hoogsteen pairing while in a wobble geometry, which was stabilized by Gln38-mediated minor groove contacts to oxoA:dGTP. Gln38Ala mutation reduced misinsertion efficiency ∼55-fold, indicating oxoA:dGTP misincorporation was promoted by minor groove interactions. Also, the efficiency of oxoA:dGTP insertion by the X-family polβ decreased ∼380-fold when Asn279-mediated minor groove contact to dGTP was abolished. Overall, these results suggest that, unlike oxoG, oxoA-mediated mutagenesis is greatly induced by minor groove interactions.

Minor Groove Site Coordination of Adenine by Platinum Group Metal Ions:  Effects on Basicity, Base Pairing, and Electronic Structure

2003 ◽  
Vol 42 (9) ◽  
pp. 3047-3056 ◽  
Author(s):  
David Amantia ◽  
Clayton Price ◽  
Michelle A. Shipman ◽  
Mark R. J. Elsegood ◽  
William Clegg ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Metal Ions ◽  
Platinum Group Metal ◽  
Minor Groove ◽  
Base Pairing ◽  
Group Metal ◽  
Platinum Group

scholarly journals Replication past a trans-4-Hydroxynonenal Minor-Groove Adduct by the Sequential Action of Human DNA Polymerases ι and κ

2006 ◽  
Vol 26 (1) ◽  
pp. 381-386 ◽  
Author(s):  
William T. Wolfle ◽  
Robert E. Johnson ◽  
Irina G. Minko ◽  
R. Stephen Lloyd ◽  
Satya Prakash ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Minor Groove ◽  
Structural Features ◽  
Lesion Site ◽  
Base Pairing ◽  
General Applicability ◽  
Sequential Action ◽  
Human Dna ◽  
Hoogsteen Base Pairing ◽  
Dna Polymerase Ι

ABSTRACT The X-ray crystal structure of human DNA polymerase ι (Polι) has shown that it differs from all known Pols in its dependence upon Hoogsteen base pairing for synthesizing DNA. Hoogsteen base pairing provides an elegant mechanism for synthesizing DNA opposite minor-groove adducts that present a severe block to synthesis by replicative DNA polymerases. Germane to this problem, a variety of DNA adducts form at the N2 minor-groove position of guanine. Previously, we have shown that proficient and error-free replication through the γ-HOPdG (γ-hydroxy-1,N 2-propano-2′-deoxyguanosine) adduct, which is formed from the reaction of acrolein with the N2 of guanine, is mediated by the sequential action of human Polι and Polκ, in which Polι incorporates the nucleotide opposite the lesion site and Polκ carries out the subsequent extension reaction. To test the general applicability of these observations to other adducts formed at the N2 position of guanine, here we examine the proficiency of human Polι and Polκ to synthesize past stereoisomers of trans-4-hydroxy-2-nonenal-deoxyguanosine (HNE-dG). Even though HNE- and acrolein-modified dGs share common structural features, due to their increased size and other structural differences, HNE adducts are potentially more blocking for replication than γ-HOPdG. We show here that the sequential action of Polι and Polκ promotes efficient and error-free synthesis through the HNE-dG adducts, in which Polι incorporates the nucleotide opposite the lesion site and Polκ performs the extension reaction.

Modified OligoDNA Having Two Consecutive Silylated-pyrene Moieties in Minor Groove Exhibiting an Excimer Fluorescent Signal upon Binding to Fully Complementary DNA Strand

2010 ◽  
Vol 39 (12) ◽  
pp. 1254-1255 ◽  
Author(s):  
Mika Mogi ◽  
Md. Gias Uddin ◽  
Mayumi Ichimura ◽  
Tomohisa Moriguchi ◽  
Kazuo Shinozuka
Keyword(s):  
Minor Groove ◽  
Complementary Dna ◽  
Fluorescent Signal ◽  
Dna Strand
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