scholarly journals Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

2012 ◽  
Vol 8 (7) ◽  
pp. 2506-2520 ◽  
Author(s):  
Miroslav Krepl ◽  
Marie Zgarbová ◽  
Petr Stadlbauer ◽  
Michal Otyepka ◽  
Pavel Banáš ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Force Field ◽  
Quadruplex Dna ◽  
Amber Force Field ◽  
Dna Quadruplex ◽  
Z Dna

Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

2011 ◽  
Vol 64 (6) ◽  
pp. 671 ◽  
Author(s):  
Chandramathi R. Sherman Durai ◽  
Margaret M. Harding
Keyword(s):  
Nucleic Acids ◽  
Combinatorial Chemistry ◽  
Self Assembly ◽  
Block Design ◽  
Quadruplex Dna ◽  
Dynamic Combinatorial Chemistry ◽  
Lead Compounds ◽  
Dna And Rna ◽  
Target Nucleic Acid ◽  
Dna Quadruplex

Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.

scholarly journals Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers

2007 ◽  
Vol 92 (11) ◽  
pp. 3817-3829 ◽  
Author(s):  
Alberto Pérez ◽  
Iván Marchán ◽  
Daniel Svozil ◽  
Jiri Sponer ◽  
Thomas E. Cheatham ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Force Field ◽  
Amber Force Field

Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters

2012 ◽  
Vol 8 (3) ◽  
pp. 948-958 ◽  
Author(s):  
Arnau Cordomí ◽  
Gianluigi Caltabiano ◽  
Leonardo Pardo
Keyword(s):  
Membrane Protein ◽  
Force Field ◽  
Amber Force Field ◽  
Lipid Parameters

VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems

2016 ◽  
Vol 56 (4) ◽  
pp. 811-818 ◽  
Author(s):  
Suqing Zheng ◽  
Qing Tang ◽  
Jian He ◽  
Shiyu Du ◽  
Shaofang Xu ◽  
...  
Keyword(s):  
Force Field ◽  
Amber Force Field ◽  
Molecular Systems ◽  
Force Field Parameters

scholarly journals Encapsulation and Ultrasound-Triggered Release of G-Quadruplex DNA in Multilayer Hydrogel Microcapsules

Polymers ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 1342 ◽  
Author(s):  
Aaron Alford ◽  
Brenna Tucker ◽  
Veronika Kozlovskaya ◽  
Jun Chen ◽  
Nirzari Gupta ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Defense Mechanisms ◽  
The Body ◽  
Stimuli Responsive ◽  
Triggered Release ◽  
Quadruplex Dna ◽  
Nucleic Acid Therapeutics ◽  
Wide Range ◽  
G Quadruplex ◽  
Hydrogel Capsules

Nucleic acid therapeutics have the potential to be the most effective disease treatment strategy due to their intrinsic precision and selectivity for coding highly specific biological processes. However, freely administered nucleic acids of any type are quickly destroyed or rendered inert by a host of defense mechanisms in the body. In this work, we address the challenge of using nucleic acids as drugs by preparing stimuli responsive poly(methacrylic acid)/poly(N-vinylpyrrolidone) (PMAA/PVPON)n multilayer hydrogel capsules loaded with ~7 kDa G-quadruplex DNA. The capsules are shown to release their DNA cargo on demand in response to both enzymatic and ultrasound (US)-triggered degradation. The unique structure adopted by the G-quadruplex is essential to its biological function and we show that the controlled release from the microcapsules preserves the basket conformation of the oligonucleotide used in our studies. We also show that the (PMAA/PVPON) multilayer hydrogel capsules can encapsulate and release ~450 kDa double stranded DNA. The encapsulation and release approaches for both oligonucleotides in multilayer hydrogel microcapsules developed here can be applied to create methodologies for new therapeutic strategies involving the controlled delivery of sensitive biomolecules. Our study provides a promising methodology for the design of effective carriers for DNA vaccines and medicines for a wide range of immunotherapies, cancer therapy and/or tissue regeneration therapies in the future.

scholarly journals A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1995 ◽  
Vol 117 (19) ◽  
pp. 5179-5197 ◽  
Author(s):  
Wendy D. Cornell ◽  
Piotr Cieplak ◽  
Christopher I. Bayly ◽  
Ian R. Gould ◽  
Kenneth M. Merz ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Force Field ◽  
Second Generation ◽  
Organic Molecules

scholarly journals Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

2020 ◽  
Vol 76 (1) ◽  
pp. 51-62 ◽  
Author(s):  
Nigel W. Moriarty ◽  
Pawel A. Janowski ◽  
Jason M. Swails ◽  
Hai Nguyen ◽  
Jane S. Richardson ◽  
...  
Keyword(s):  
Force Field ◽  
Active Sites ◽  
Protein Structures ◽  
Target Function ◽  
Real Space ◽  
Model Quality ◽  
Nonbonded Interactions ◽  
Amber Force Field ◽  
Quantum Mechanical Representation ◽  
Improved Model

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard–Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing.

GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Soft Matter ◽  
2012 ◽  
Vol 8 (37) ◽  
pp. 9617 ◽  
Author(s):  
Callum J. Dickson ◽  
Lula Rosso ◽  
Robin M. Betz ◽  
Ross C. Walker ◽  
Ian R. Gould
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Dynamics Simulation ◽  
Amber Force Field
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