Molecular Determinants for DNA Minor Groove Recognition:  Design of a Bis-Guanidinium Derivative of Ethidium That Is Highly Selective for AT-Rich DNA Sequences†

Biochemistry ◽  
2005 ◽  
Vol 44 (6) ◽  
pp. 1941-1952 ◽  
Author(s):  
Christian Bailly ◽  
Reem K. Arafa ◽  
Farial A. Tanious ◽  
William Laine ◽  
Christèle Tardy ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Minor Groove ◽  
Dna Minor Groove ◽  
Molecular Determinants

scholarly journals Conditional Cooperativity in DNA Minor-Groove Recognition by Oligopeptides

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5188
Author(s):  
Jurij Lah ◽  
San Hadži
Keyword(s):  
Phase Diagrams ◽  
Transcription Regulation ◽  
Thermodynamic Analysis ◽  
Dna Sequences ◽  
Minor Groove ◽  
Ion Concentration ◽  
Cooperative Binding ◽  
Dna Minor Groove ◽  
Molecular Interpretation ◽  
Regulation Mechanisms

The recognition of specific DNA sequences in processes such as transcription is associated with a cooperative binding of proteins. Some transcription regulation mechanisms involve additional proteins that can influence the binding cooperativity by acting as corepressors or coactivators. In a conditional cooperativity mechanism, the same protein can induce binding cooperativity at one concentration and inhibit it at another. Here, we use calorimetric (ITC) and spectroscopic (UV, CD) experiments to show that such conditional cooperativity can also be achieved by the small DNA-directed oligopeptides distamycin and netropsin. Using a global thermodynamic analysis of the observed binding and (un)folding processes, we calculate the phase diagrams for this system, which show that distamycin binding cooperativity is more pronounced at lower temperatures and can be first induced and then reduced by increasing the netropsin or/and Na+ ion concentration. A molecular interpretation of this phenomenon is suggested.

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).

Design and Synthesis of a Peptide That Binds Specific DNA Sequences through Simultaneous Interaction in the Major and in the Minor Groove

2001 ◽  
Vol 113 (24) ◽  
pp. 4859-4861 ◽  
Author(s):  
M. Eugenio Vázquez ◽  
Ana M. Caamaño ◽  
José Martínez-Costas ◽  
Luis Castedo ◽  
José L. Mascareñas
Keyword(s):  
Dna Sequences ◽  
Minor Groove ◽  
Design And Synthesis
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