scholarly journals HMG-D complexed to a bulge DNA: An NMR model

2001 ◽  
Vol 10 (3) ◽  
pp. 504-518 ◽  
Author(s):  
R. Cerdan
Keyword(s):  
Bulge Dna

A 2,7-diamino-1,4,8-triazanaphthalene derivative selectively binds to cytosine bulge DNA only at a weakly acidic pH

2017 ◽  
Vol 15 (6) ◽  
pp. 1313-1316 ◽  
Author(s):  
H. Aikawa ◽  
A. Yano ◽  
K. Nakatani
Keyword(s):  
Acidic Ph ◽  
Dna Duplex ◽  
Ph Profile ◽  
Selective Binding ◽  
Absorption Change ◽  
Bulge Dna ◽  
Acidic Conditions

2,7-Diamino-1,4,8-triazanaphthalene (azaDANP) shows selective binding to a cytosine bulge DNA duplex under weakly acidic conditions, and the absorption change of azaDANP on binding to the target is very sensitive to environmental pH with a bell-shaped absorption–pH profile.

scholarly journals Structural insights into DNA repair by RNase T

2014 ◽  
Vol 70 (a1) ◽  
pp. C208-C208
Author(s):  
Yu-Yuan Hsiao ◽  
Hanna Yuan
Keyword(s):  
Crystal Structure ◽  
Dna Repair ◽  
Binding Mode ◽  
Heteroduplex Dna ◽  
Dna Enzymes ◽  
Endonuclease V ◽  
Dna Damaging Agents ◽  
Bulge Dna ◽  
Repair Pathways ◽  
Structural Insights

DNA repair is generally accomplished by a coordinated effort via several types of DNA enzymes, including endonucleases, exonucleases, helicases, polymerases and ligases. Among all these DNA enzymes, the molecular functions of exonucleases, which bind at the 3′ or 5′ end of DNA and cleave one nucleotide at a time, are least understood in how they select DNA substrates for binding and trimming. Here we show that the DEDDh family exonuclease RNase T is critical for Escherichia coli resistance to various DNA damaging agents and UV radiation. RNase T specifically trims the 3′ end of structured DNA, including bulge, bubble and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Our crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3′ end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3′ overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V-dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DEDDh-family exonucleases in DNA 3′-end processing.

Synthesis and Photophysical Properties of Fluorescence Molecular Probe for Turn-ON-Type Detection of Cytosine Bulge DNA

2016 ◽  
Vol 18 (13) ◽  
pp. 3170-3173 ◽  
Author(s):  
Rajiv Kumar Verma ◽  
Fumie Takei ◽  
Kazuhiko Nakatani
Keyword(s):  
Photophysical Properties ◽  
Molecular Probe ◽  
Turn On ◽  
Bulge Dna

New Complex of Post-Activated Neocarzinostatin Chromophore with DNA:  Bulge DNA Binding from the Minor Groove†

Biochemistry ◽  
2003 ◽  
Vol 42 (5) ◽  
pp. 1186-1198 ◽  
Author(s):  
Youngjoo Kwon ◽  
Zhen Xi ◽  
Lizzy S. Kappen ◽  
Irving H. Goldberg ◽  
Xiaolian Gao
Keyword(s):  
Dna Binding ◽  
Minor Groove ◽  
Bulge Dna
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