Determining the topology of stable protein–DNA complexes

2013 ◽  
Vol 41 (2) ◽  
pp. 601-605 ◽  
Author(s):  
Isabel K. Darcy ◽  
Mariel Vazquez
Keyword(s):  
Present Article ◽  
Experimental Technique ◽  
Topological Structure ◽  
Reaction Pathway ◽  
Dna Supercoiling ◽  
Dna Complexes ◽  
Nucleoprotein Complex ◽  
Mu Transpososome ◽  
Dna Complex

Difference topology is an experimental technique that can be used to unveil the topological structure adopted by two or more DNA segments in a stable protein–DNA complex. Difference topology has also been used to detect intermediates in a reaction pathway and to investigate the role of DNA supercoiling. In the present article, we review difference topology as applied to the Mu transpososome. The tools discussed can be applied to any stable nucleoprotein complex.

scholarly journals A topological analysis of difference topology experiments of condensin with Topoisomerases II

2019 ◽  
Author(s):  
Soojeong Kim ◽  
Isabel K. Darcy
Keyword(s):  
Simple Model ◽  
Experimental Technique ◽  
Topological Analysis ◽  
Simple Experiment ◽  
Dna Complexes ◽  
3 Dimensional ◽  
Model Protein ◽  
Summary Statement ◽  
Mu Transpososome ◽  
Dimensional Ball

ABSTRACTAn experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the Mu transpososome. However, difference topology experiments can be difficult and time-consuming. We discuss a modification that greatly simplifies this experimental technique. This simple experiment involves using a topoisomerase to trap DNA crossings bound by a protein complex and then running a gel to determine the crossing number of the knotted product(s). We develop the mathematics needed to analyze the results and apply these results to model the topology of DNA bound by 13S condensin and by the condensin MukB.SUMMARY STATEMENTTangles are used to model protein-DNA complexes: A 3-dimensional ball represents protein while strings embedded in this ball represent protein-bound DNA. We use this simple model to analyze experimental results.

Modelling of DNA Complexes with Distamycin Analogues Using an ab initio Continuum Solvent Model

2000 ◽  
Vol 65 (5) ◽  
pp. 631-643 ◽  
Author(s):  
Petr Bouř ◽  
Vladimír Král
Keyword(s):  
Complex Formation ◽  
Ab Initio ◽  
Polar Solvent ◽  
Molecular Shape ◽  
Conformational Flexibility ◽  
Model Systems ◽  
Dna Complexes ◽  
Solvent Model ◽  
Dna Complex

Model systems related to non-covalent minor groove DNA complexes with distamycin analogues were investigated using the Turbomole and Gaussian quantum chemical packages. The role of molecular shape, electrostatic field and conformer energies in the complex formation was discussed. The ab initio calculations included the COSMO solvent model. If compared to vacuum computations, polar solvent significantly destabilizes such complexes and increases conformational flexibility of distamycin. The DNA complex formation appears to be driven mainly by entropy lowering and complementarity of molecular shapes. The NH moiety of the amide group preferably points to the base pair according to the computations, in agreement with experimental data.

An approach to the clinical manifestation of Rupavriddhi Rupahani Rupantara in Avarana

2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Dr. Sharanamma . ◽  
Dr. A. S. Prashanth ◽  
Dr. S. G. Chavan
Keyword(s):  
Clinical Practice ◽  
Clinical Study ◽  
Present Article ◽  
Clinical Manifestation ◽  
Basic Concept ◽  
Favorable Condition ◽  
Wrong Diagnosis

Ayurveda believes in different pathology which sets in different Srotas to produce different diseases. Whenever a favorable condition and situation arise, diseases will manifest. Nanatmaja Vikara, Anubandha, Gatavata and Avarana are different pathologies explained in Ayurveda. Avarana is one of the most difficult concept to understand teach and incorporate in clinical practice. It is either least observed, diagnosed or goes unidentified due to lack of skill. To understand and analyze the Avarana, Meticulous knowledge of basic concept of Ayurveda is essential. It is assumed that symptoms complex in Avarana leads to misunderstanding, wrong diagnosis and sometimes end with complications. The symptoms produced in Avarana are based on the principles of Rupahani (Karmakshaya), Rupavriddi (Karmavriddhi) and Rupantara (Anya Karma). The present article is an attempt made to have a critical clinical study of role of Avarana in the manifestation of Rupavriddhi, Rupahani, Rupantara.

scholarly journals The Role of lncRNA in the Development of Tumors, Including Breast Cancer

2021 ◽  
Vol 22 (16) ◽  
pp. 8427
Author(s):  
Beata Smolarz ◽  
Anna Zadrożna-Nowak ◽  
Hanna Romanowicz
Keyword(s):  
Breast Cancer ◽  
Breast Carcinoma ◽  
Present Article ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Regulation Of Transcription ◽  
Ribonucleic Acids ◽  
Detailed Review ◽  
Cellular Processes

Long noncoding RNAs (lncRNAs) are the largest groups of ribonucleic acids, but, despite the increasing amount of literature data, the least understood. Given the involvement of lncRNA in basic cellular processes, especially in the regulation of transcription, the role of these noncoding molecules seems to be of great importance for the proper functioning of the organism. Studies have shown a relationship between disturbed lncRNA expression and the pathogenesis of many diseases, including cancer. The present article presents a detailed review of the latest reports and data regarding the importance of lncRNA in the development of cancers, including breast carcinoma.

Ethanol conversion over Ga2O3-ZrO2 solid solution: empirical evidences of the reaction pathway, the surface acid–base property, and role of isolated gallium ion

2021 ◽  
Author(s):  
Takashi Yamamoto ◽  
Akihito Kurimoto ◽  
Riona Sato ◽  
Shoki Katada ◽  
Hirotaka Mine ◽  
...  
Keyword(s):  
Solid Solution ◽  
Reaction Pathway ◽  
Ethanol Conversion ◽  
Acid Base ◽  
Base Property ◽  
Temperature Range ◽  
Acid Base Property

Ethanol conversion by Ga2O3-ZrO2 solid solution was examined in the temperature range 573–773 K, and acetone/isobutene formation was confirmed under cofeeding of H2O vapor. The reaction pathway was empirically investigated...

scholarly journals A room with a view: a special issue with a special perspective

2021 ◽  
Vol 26 (3) ◽  
pp. 205-210
Author(s):  
Simone Borghesi
Keyword(s):  
Climate Change ◽  
Developing Countries ◽  
Climate Policy ◽  
Present Article ◽  
Emerging Economies ◽  
Emissions Trading ◽  
Developed Countries ◽  
Special Issue ◽  
Climate Policies

AbstractThe present article describes the main insights deriving from the papers collected in this special issue which jointly provide a ‘room with a view’ on some of the most relevant issues in climate policy such as: the role of uncertainty, the distributional implications of climate change, the drivers and applications of decarbonizing innovation, the role of emissions trading and its interactions with companion policies. While looking at different issues and from different angles, all papers share a similar attention to policy aspects and implications, especially in developing countries. This is particularly important to evaluate whether and to what extent the climate policies adopted thus far in developed countries can be replicated in emerging economies.

Role of Multivalent Cations in the Self-Assembly of Phospholipid−DNA Complexes

2007 ◽  
Vol 111 (51) ◽  
pp. 14233-14238 ◽  
Author(s):  
Guillaume Tresset ◽  
Wun Chet Davy Cheong ◽  
Yeng Ming Lam
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Dna Complexes

The role of hydrophobic alkyl chains in the physicochemical properties of poly(β-amino ester)/DNA complexes

2015 ◽  
Vol 126 ◽  
pp. 374-380 ◽  
Author(s):  
Azahara Rata-Aguilar ◽  
Nathaly Segovia-Ramos ◽  
Ana Belén Jódar-Reyes ◽  
Víctor Ramos-Pérez ◽  
Salvador Borrós ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Amino Ester ◽  
Dna Complexes ◽  
Alkyl Chains
Sign in / Sign up

Export Citation Format

Share Document