Stability and Polymerase Recognition of Pyridine Nucleobase Analogues: Role of Minor-Groove H-Bond Acceptors

2006 ◽  
Vol 118 (46) ◽  
pp. 7973-7976 ◽  
Author(s):  
Yoonkyung Kim ◽  
Aaron M. Leconte ◽  
Yoshiyuki Hari ◽  
Floyd E. Romesberg
Keyword(s):  
Minor Groove

scholarly journals Role of Minor Groove Width and Hydration Pattern on Amsacrine Interaction with DNA

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e69933 ◽  
Author(s):  
Deepak K. Jangir ◽  
Suman Kundu ◽  
Ranjana Mehrotra
Keyword(s):  
Minor Groove ◽  
Groove Width

Comparison of the biological effects of MMS and Me-lex, a minor groove methylating agent: Clarifying the role of N3-methyladenine

2014 ◽  
Vol 759 ◽  
pp. 45-51 ◽  
Author(s):  
Paola Monti ◽  
Giorgia Foggetti ◽  
Paola Menichini ◽  
Alberto Inga ◽  
Barry Gold ◽  
...  
Keyword(s):  
Biological Effects ◽  
Minor Groove ◽  
A Minor

Short Lexitropsin that Recognizes the DNA Minor Groove at 5‘-ACTAGT-3‘:  Understanding the Role of Isopropyl-thiazole

2004 ◽  
Vol 126 (36) ◽  
pp. 11338-11349 ◽  
Author(s):  
Nahoum G. Anthony ◽  
Blair F. Johnston ◽  
Abedawn I. Khalaf ◽  
Simon P. MacKay ◽  
John A. Parkinson ◽  
...  
Keyword(s):  
Minor Groove ◽  
Dna Minor Groove

scholarly journals Importance of base-pair opening for mismatch recognition

2020 ◽  
Vol 48 (20) ◽  
pp. 11322-11334
Author(s):  
Tomáš Bouchal ◽  
Ivo Durník ◽  
Viktor Illík ◽  
Kamila Réblová ◽  
Petr Kulhánek
Keyword(s):  
Base Pair ◽  
Computational Study ◽  
Minor Groove ◽  
Base Pairs ◽  
Theoretical Support ◽  
Molecular Pattern ◽  
Anti Cancer ◽  
Mismatch Recognition ◽  
Base Pair Opening

Abstract Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.

scholarly journals Efficient and Error-Free Replication past a Minor-Groove N2-Guanine Adduct by the Sequential Action of Yeast Rev1 and DNA Polymerase ζ

2004 ◽  
Vol 24 (16) ◽  
pp. 6900-6906 ◽  
Author(s):  
M. Todd Washington ◽  
Irina G. Minko ◽  
Robert E. Johnson ◽  
Lajos Haracska ◽  
Thomas M. Harris ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Close Contact ◽  
Dna Polymerases ◽  
Minor Groove ◽  
Synthetic Activity ◽  
Oxidation Reactions ◽  
Lesion Bypass ◽  
Dna Minor Groove

ABSTRACT Rev1, a member of the Y family of DNA polymerases, functions in lesion bypass together with DNA polymerase ζ (Polζ). Rev1 is a highly specialized enzyme in that it incorporates only a C opposite template G. While Rev1 plays an indispensable structural role in Polζ-dependent lesion bypass, the role of its DNA synthetic activity in lesion bypass has remained unclear. Since interactions of DNA polymerases with the DNA minor groove contribute to the nearly equivalent efficiencies and fidelities of nucleotide incorporation opposite each of the four template bases, here we examine the possibility that unlike other DNA polymerases, Rev1 does not come into close contact with the minor groove of the incipient base pair, and that enables it to incorporate a C opposite the N 2-adducted guanines in DNA. To test this idea, we examined whether Rev1 could incorporate a C opposite the γ-hydroxy-1,N 2-propano-2′deoxyguanosine DNA minor-groove adduct, which is formed from the reaction of acrolein with the N 2 of guanine. Acrolein, an α,β-unsaturated aldehyde, is generated in vivo as the end product of lipid peroxidation and from other oxidation reactions. We show here that Rev1 efficiently incorporates a C opposite this adduct from which Polζ subsequently extends, thereby completing the lesion bypass reaction. Based upon these observations, we suggest that an important role of the Rev1 DNA synthetic activity in lesion bypass is to incorporate a C opposite the various N 2-guanine DNA minor-groove adducts that form in DNA.

NMR Studies of DNA Support the Role of Pre-Existing Minor Groove Variations in Nucleosome Indirect Readout

Biochemistry ◽  
2014 ◽  
Vol 53 (35) ◽  
pp. 5601-5612 ◽  
Author(s):  
Xiaoqian Xu ◽  
Akli Ben Imeddourene ◽  
Loussiné Zargarian ◽  
Nicolas Foloppe ◽  
Olivier Mauffret ◽  
...  
Keyword(s):  
Minor Groove ◽  
Nmr Studies ◽  
Indirect Readout

scholarly journals Design, synthesis and antibacterial activity of minor groove binders: The role of non-cationic tail groups

2012 ◽  
Vol 56 ◽  
pp. 39-47 ◽  
Author(s):  
Abedawn I. Khalaf ◽  
Claire Bourdin ◽  
David Breen ◽  
Gavin Donoghue ◽  
Fraser J. Scott ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Minor Groove ◽  
Design Synthesis ◽  
Minor Groove Binders ◽  
Groove Binders
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