Special Issue "Nucleic Acid Dynamics and Structure"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: 1 December 2018

Special Issue Editor

Guest Editor
Prof. Dr. Ishita Mukerji

Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA
Website | E-Mail
Interests: DNA structure, DNA dynamics, fluorescence spectroscopy, FRET, molecular dynamics simulations, thermodynamcis, protein-DNA interactions, DNA repair

Special Issue Information

Dear Colleagues,

Recognition of nucleic acid substrates by proteins is often governed by their relative stability and local dynamics. In addition, many nucleic acid substrates, particularly RNA-based ones adopt complex structures the stability of which are often governed by function and mediated by ligand binding. For example, RNA riboswitches in the presence of one ligand will adopt one structure, while adopting a non-functional form in the absence of ligand. In a given ensemble, highly sampled states are often associated with binding interactions; although conformational capture of a rarely sampled state by binding of protein or a ligand can be another mechanism for forming a functional state. This volume will explore relationships wherein the dynamics of the nucleic acid is an important element of adopting a functional conformation. In this Special Issue, we welcome submissions of original articles as well as reviews of any topics that consider conformational dynamics and thermodynamics related to protein and ligand binding, aptamer selection, allostery and overall function for a better understanding of nucleic acid structure and dynamics including new perspectives and interpretations as well as novel technological and theoretical findings.

Prof. Dr. Ishita Mukerji
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • Structure
  • dynamics
  • allostery
  • structure-function
  • specificity and recognition
  • protein-induced bending
  • conformational dynamic
  • induced fit

Published Papers (1 paper)

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Open AccessArticle Kinetics and Thermodynamics of DNA Processing by Wild Type DNA-Glycosylase Endo III and Its Catalytically Inactive Mutant Forms
Received: 27 February 2018 / Revised: 22 March 2018 / Accepted: 27 March 2018 / Published: 30 March 2018
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Endonuclease III (Endo III or Nth) is one of the key enzymes responsible for initiating the base excision repair of oxidized or reduced pyrimidine bases in DNA. In this study, a thermodynamic analysis of structural rearrangements of the specific and nonspecific DNA-duplexes during
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Endonuclease III (Endo III or Nth) is one of the key enzymes responsible for initiating the base excision repair of oxidized or reduced pyrimidine bases in DNA. In this study, a thermodynamic analysis of structural rearrangements of the specific and nonspecific DNA-duplexes during their interaction with Endo III is performed based on stopped-flow kinetic data. 1,3-diaza-2-oxophenoxazine (tCO), a fluorescent analog of the natural nucleobase cytosine, is used to record multistep DNA binding and lesion recognition within a temperature range (5–37 °C). Standard Gibbs energy, enthalpy, and entropy of the specific steps are derived from kinetic data using Van’t Hoff plots. The data suggest that enthalpy-driven exothermic 5,6-dihydrouracil (DHU) recognition and desolvation-accompanied entropy-driven adjustment of the enzyme–substrate complex into a catalytically active state play equally important parts in the overall process. The roles of catalytically significant amino acids Lys120 and Asp138 in the DNA lesion recognition and catalysis are identified. Lys120 participates not only in the catalytic steps but also in the processes of local duplex distortion, whereas substitution Asp138Ala leads to a complete loss of the ability of Endo III to distort a DNA double chain during enzyme–DNA complex formation. Full article
(This article belongs to the Special Issue Nucleic Acid Dynamics and Structure)

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