scholarly journals Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition

2016 ◽  
Vol 44 (10) ◽  
pp. 4519-4527 ◽  
Author(s):  
Narinder K. Harika ◽  
Ananya Paul ◽  
Ekaterina Stroeva ◽  
Yun Chai ◽  
David W. Boykin ◽  
...  
Keyword(s):  
Base Pair ◽  
Proton Nmr ◽  
Minor Groove ◽  
Imino Proton ◽  
Minor Groove Binders ◽  
Groove Binders

Molecular mechanics calculations on the complexes between analogues of Hoechst 33258 and d(CGCGAAT-TCGCG)2: influence of bulky group substitution on base pair preference of DNA minor groove binders

1995 ◽  
Vol 73 (6) ◽  
pp. 878-884 ◽  
Author(s):  
Ding-Kwo Chang ◽  
Shu-Fang Cheng ◽  
Ting-Lin Chien
Keyword(s):  
Molecular Mechanics ◽  
Base Pair ◽  
Minor Groove ◽  
Sequence Specificity ◽  
Hoechst 33258 ◽  
Molecular Mechanics Calculations ◽  
Dna Minor Groove ◽  
Minor Groove Binders ◽  
Detailed Structural Analysis ◽  
Groove Binders

Molecular mechanics calculations were performed on the three structures of the complexes formed by the derivatives of Hoechst 33258 and dodecameric DNA duplex d(CGCGAATTCGCG)2. Formation and docking energies of these complexes were compared. It was found that the CG site that is 3′ to the central AATT region can be tolerated by the drugs. This is probably due to the presence of the bulky piperazine ring and, more pronouncedly, by alkylated analogues of the drug that prefer the wider minor groove formed by the GC base pair region of B-DNA. The argument of bulkiness of the piperazine moiety as the origin of enhancement of GC affinity is supported by detailed structural analysis of the intermolecular interface and widening of the DNA minor groove at the binding site. Implications of the results are discussed. Keywords: minor groove binder, docking energy, sequence specificity.

scholarly journals Mixed up minor groove binders: Convincing A·T specific compounds to recognize a G·C base pair

2015 ◽  
Vol 25 (21) ◽  
pp. 4927-4932 ◽  
Author(s):  
Ananya Paul ◽  
Rupesh Nanjunda ◽  
Arvind Kumar ◽  
Sarah Laughlin ◽  
Raja Nhili ◽  
...  
Keyword(s):  
Base Pair ◽  
Minor Groove ◽  
Minor Groove Binders ◽  
Groove Binders

scholarly journals Dissociation of minor groove binders from DNA: insights from metadynamics simulations

2008 ◽  
Vol 36 (18) ◽  
pp. 5910-5921 ◽  
Author(s):  
A. V. Vargiu ◽  
P. Ruggerone ◽  
A. Magistrato ◽  
P. Carloni
Keyword(s):  
Minor Groove ◽  
Minor Groove Binders ◽  
Groove Binders

scholarly journals An evaluation of Minor Groove Binders as anti-fungal and anti-mycobacterial therapeutics

2017 ◽  
Vol 136 ◽  
pp. 561-572 ◽  
Author(s):  
Fraser J. Scott ◽  
Ryan J.O. Nichol ◽  
Abedawn I. Khalaf ◽  
Federica Giordani ◽  
Kirsten Gillingwater ◽  
...  
Keyword(s):  
Minor Groove ◽  
Minor Groove Binders ◽  
Anti Fungal ◽  
Groove Binders

Conjugates between minor groove binders and Zn(II)-tach complexes: Synthesis, characterization, and interaction with plasmid DNA

Tetrahedron ◽  
2017 ◽  
Vol 73 (21) ◽  
pp. 3014-3024 ◽  
Author(s):  
Claudia Sissi ◽  
Luca Dovigo ◽  
Maria Laura Greco ◽  
Antonella Ciancetta ◽  
Stefano Moro ◽  
...  
Keyword(s):  
Plasmid Dna ◽  
Minor Groove ◽  
Minor Groove Binders ◽  
Groove Binders

scholarly journals Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

2016 ◽  
Vol 12 ◽  
pp. 1348-1360 ◽  
Author(s):  
Svetlana V Vasilyeva ◽  
Vyacheslav V Filichev ◽  
Alexandre S Boutorine
Keyword(s):  
Minor Groove ◽  
Binding Parameters ◽  
Design And Synthesis ◽  
Minor Groove Binders ◽  
Double Stranded Dna ◽  
Triple Helices ◽  
Gel Shift ◽  
Groove Binders

Efficient protocols based on Cu(I)-catalyzed azide–alkyne cycloaddition were developed for the synthesis of conjugates of pyrrole–imidazole polyamide minor groove binders (MGB) with fluorophores and with triplex-forming oligonucleotides (TFOs). Diverse bifunctional linkers were synthesized and used for the insertion of terminal azides or alkynes into TFOs and MGBs. The formation of stable triple helices by TFO-MGB conjugates was evaluated by gel-shift experiments. The presence of MGB in these conjugates did not affect the binding parameters (affinity and triplex stability) of the parent TFOs.

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