A thermodynamic and structural analysis of DNA minor-groove complex formation 1 1Edited by I. Tinoco

2000 ◽  
Vol 300 (2) ◽  
pp. 321-337 ◽  
Author(s):  
Suzann Mazur ◽  
Farial A. Tanious ◽  
Daoyuan Ding ◽  
Arvind Kumar ◽  
David W. Boykin ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Complex Formation ◽  
Minor Groove ◽  
Dna Minor Groove

scholarly journals Molecular modelling of the interaction of carbocyclic analogues of netropsin and distamycin with d(CGCGAATTCGCG)2.

2000 ◽  
Vol 47 (3) ◽  
pp. 855-866 ◽  
Author(s):  
K Bielawski ◽  
A Bielawska ◽  
D Bartulewicz ◽  
A Rózański
Keyword(s):  
Molecular Structure ◽  
Molecular Dynamics ◽  
Complex Formation ◽  
Hydrogen Bonds ◽  
Electrostatic Interactions ◽  
Minor Groove ◽  
Model Complexes ◽  
Dna Minor Groove ◽  
Energetic Analysis ◽  
Effective Penetration

A molecular mechanics and molecular dynamics approach was used to examine the structure of complexes formed between the d(CGCGAATTCGCG)2 duplex and netropsin, distamycin, and four carbocyclic analogues of netropsin and distamycin (1-4). The resulting structures of the ligand-DNA model complexes and their energetics were examined. It is predicted that the compounds 1-4 should have a decreased affinity for the minor groove of AT-rich regions in comparison to netropsin and distamycin. From the energetic analysis it appears that van der Waals and electrostatic interactions are more important than specific hydrogen bonds in stabilizing the ligand-duplex complexes. We predict that compounds 1 and 2 are effectively isohelical with the DNA minor groove. The superior DNA-binding afforded by 1 and 2 in comparison to 3 and 4 results from their more effective penetration into the minor groove and smaller perturbation of molecular structure upon complex formation.

scholarly journals Cellular pharmacology of novel C8-linked anthramycin-based sequence-selective DNA minor groove cross-linking agents

1994 ◽  
Vol 70 (1) ◽  
pp. 48-53 ◽  
Author(s):  
M Smellie ◽  
LR Kelland ◽  
DE Thurston ◽  
RL Souhami ◽  
JA Hartley
Keyword(s):  
Minor Groove ◽  
Cross Linking ◽  
Dna Minor Groove ◽  
Cellular Pharmacology

Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin

2011 ◽  
Vol 17 (11) ◽  
pp. 2805-2816 ◽  
Author(s):  
Mathew Varghese Koonammackal ◽  
Unnikrishnan Viswambharan Nair Nellipparambil ◽  
Chellappanpillai Sudarsanakumar
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Analysis ◽  
Binding Free Energy ◽  
Minor Groove ◽  
Dna Minor Groove ◽  
Dynamics Simulations ◽  
Free Energy Analysis

Influence of GC and AT Specific DNA Minor Groove Binding Drugs on Intermolecular Triplex Formation in the Human c-Ki-ras Promoter†

Biochemistry ◽  
1996 ◽  
Vol 35 (4) ◽  
pp. 1106-1114 ◽  
Author(s):  
Nadarajah Vigneswaran ◽  
Charles A. Mayfield ◽  
Brad Rodu ◽  
Roger James ◽  
H.-G. Kim ◽  
...  
Keyword(s):  
Minor Groove ◽  
Minor Groove Binding ◽  
Groove Binding ◽  
Dna Minor Groove ◽  
Triplex Formation

Three-centre C—H...O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures

1999 ◽  
Vol 55 (12) ◽  
pp. 2005-2012 ◽  
Author(s):  
Anirban Ghosh ◽  
Manju Bansal
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Base Pair ◽  
Minor Groove ◽  
Local Geometry ◽  
Data Sets ◽  
Base Pairs ◽  
Dna Minor Groove ◽  
Close Proximity ◽  
Using Data

AA·TT and GA·TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 Å) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA·TT and GA·TC steps the electropositive C2—H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C—H...O hydrogen bonds in the DNA minor groove. The C2—H2...O2 hydrogen bonds in the A·T base pairs could be a natural consequence of Watson–Crick pairing. However, the cross-strand interactions between the bases at the 3′-end of the AA·TT and GA·TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2...O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 Å) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A·T base pairs and the hydration of the minor groove, these C2—H2...O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA)·poly(dT).

scholarly journals DNA Minor Groove Binding with Bisbenzamidine-Ru(II) Complexes

2019 ◽  
Author(s):  
Mateo I. Sánchez ◽  
Gustavo Rama ◽  
Renata Calo ◽  
Kübra Ucar ◽  
Per Lincoln ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Coordination Compounds ◽  
Photophysical Properties ◽  
Organic Ligand ◽  
Minor Groove ◽  
The Other ◽  
Minor Groove Binding ◽  
Binding Agent ◽  
Groove Binding ◽  
Dna Minor Groove

We report the first Ru(II) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites. This was made possible by integrating a bis‑benzamidine minor groove DNA-binding agent with a ruthenium(II) complex. Importantly, one of the enantiomers (Δ‑[Ru(bpy)<sub>2</sub><b>b4bpy</b>]<sup>2+</sup>, <b>Δ‑4Ru</b>) shows a considerably higher DNA affinity than the parent organic ligand and than the other enantiomer, particularly for the AATT sequence, while the other enantiomer preferentially targets long AAATTT sites with overall lower affinity. Finally, we demonstrate that the photophysical properties of these new binders can be exploited for DNA cleavage using visible light.

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