Journal ArticleDOI
Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages.
Anna M. Varizhuk,Vladimir B. Tsvetkov,Olga N. Tatarinova,Dmitry N. Kaluzhny,V. L. Florentiev,Edward N. Timofeev,Anna K. Shchyolkina,Olga F. Borisova,Igor P. Smirnov,S. L. Grokhovsky,Anton V. Aseychev,Galina E. Pozmogova +11 more
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TLDR
Due to their relatively high activity and the increased resistance to nuclease digestion imparted by the triazole internucleotide linkages, the novel aptamers are a promising alternative to known DNA-based anticoagulant agents.About:
This article is published in European Journal of Medicinal Chemistry.The article was published on 2013-09-01. It has received 46 citations till now. The article focuses on the topics: Aptamer & Nuclease.read more
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Medicinal attributes of 1,2,3-triazoles: Current developments
TL;DR: The present work aims to summarize the current approaches adopted for the synthesis of the 1,2,3-triazole and medicinal significance of these architectures as a lead structure for the discovery of drug molecules such as COX-1/COX-2 inhibitors, HIV protease inhibitors, CB1 cannabinoid receptor antagonist and much more which are in the pipeline of clinical trials.
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Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes.
TL;DR: This review will discuss methods to conquer challenges of susceptibility to nuclease degradation, rapid excretion through renal filtration and insufficient binding affinity, and highlight recent developments of chemical modifications and technological advances that may enable early aptamers to be translated into clinical therapeutics.
Journal ArticleDOI
Aptamers Chemistry: Chemical Modifications and Conjugation Strategies.
Fadwa Odeh,Hamdi Nsairat,Walhan Alshaer,Mohammad A. Ismail,Ezaldeen Esawi,Bara’a M. Qaqish,Abeer Al Bawab,Said I. Ismail,Said I. Ismail +8 more
TL;DR: Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism, and they are superior regarding a longer shelf life, simple production and chemical modification.
Journal ArticleDOI
Investigations on the interface of nucleic acid aptamers and binding targets.
TL;DR: The binding targets of aptamers, such as small molecules, macromolecules, and even cells are summarized, and the binding forces mediating the aptamer-target interactions, including hydrogen bonding, electrostatic interaction, the hydrophobic effect, π-π stacking and van der Waals forces are summarized.
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SELEX methods on the road to protein targeting with nucleic acid aptamers.
Payam Bayat,Rahim Nosrati,Mona Alibolandi,Houshang Rafatpanah,Khalil Abnous,Mostafa Khedri,Mohammad Ramezani +6 more
TL;DR: This review will discuss the recent advances in SELEX methods and their advantages and limitations and aptamer applications are briefly outlined in this review.
References
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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
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Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
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Selection of single-stranded DNA molecules that bind and inhibit human thrombin.
TL;DR: The isolation of single-stranded DNA aptamers to the protease thrombin of the blood coagulation cascade is described and binding affinities in the range 25–200 nM are reported.
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Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
Alberto Perez,Ivan Marchán,Daniel Svozil,Daniel Svozil,Jiri Sponer,Jiri Sponer,Thomas E. Cheatham,Charles A. Laughton,Modesto Orozco +8 more
TL;DR: The parmbsc0 force field as mentioned in this paper is a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the a/g concerted rotation in nucleic acids (NAs).