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Cutting-Edge Research of Nucleic Acid Polymerases

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 1105

Special Issue Editors

New York Structural Biology Center, New York, NY 10027, USA
Interests: gene; RNA; cryo-EM; SARS-Cov-2
Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Interests: gene; DNA; cryo-EM

Special Issue Information

Dear Colleagues,

Nucleic acid polymerases are vital for DNA and RNA metabolism and play an important role in various pathways such as replication, repair, recombination, transcription and translation. In the cell, the polymerases work in synergy with an intricate network of other proteins and are inherently dynamic in nature. Modifications to these polymerases and changes in their expression may lead to alterations in cell cycle progression resulting in mutagenesis, cancer and various heritable diseases. To understand the molecular underpinnings of these biological processes, various biochemical and biophysical approaches such as single particle cryo-electron microscopy, X-ray crystallography, NMR spectroscopy and single molecule fluorescence microscopy are employed to study these polymerases. In particular, advances in cryo-electron microscopy have made it possible to derive high resolution 3-D structural information of these ever-expanding and dynamic polymerase complexes.

This special issue will cover the recent advances in the structure and dynamics of DNA and RNA polymerases, their molecular mechanisms and role in key biological processes.

Dr. Edward T Eng
Dr. Radhika Malik
Guest Editors

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 submissions that pass pre-check are 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Keywords

  • DNA polymerases
  • DNA repair
  • RNA polymerases
  • macromolecular assemblies
  • replisome
  • cancer research
  • gene regulation
  • nucleotide damage
  • mutagenesis

Published Papers (1 paper)

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Research

23 pages, 9103 KiB  
Article
Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency
by Olga A. Zasedateleva, Sergey A. Surzhikov, Viktoriya E. Kuznetsova, Valeriy E. Shershov, Victor E. Barsky, Alexander S. Zasedatelev and Alexander V. Chudinov
Int. J. Mol. Sci. 2023, 24(17), 13643; https://doi.org/10.3390/ijms241713643 - 04 Sep 2023
Viewed by 724
Abstract
The approach based on molecular modeling was developed to study dNTP derivatives characterized by new polymerase-specific properties. For this purpose, the relative efficiency of PCR amplification with modified dUTPs was studied using Taq, Tth, Pfu, Vent, Deep Vent, Vent (exo-), and Deep Vent [...] Read more.
The approach based on molecular modeling was developed to study dNTP derivatives characterized by new polymerase-specific properties. For this purpose, the relative efficiency of PCR amplification with modified dUTPs was studied using Taq, Tth, Pfu, Vent, Deep Vent, Vent (exo-), and Deep Vent (exo-) DNA polymerases. The efficiency of PCR amplification with modified dUTPs was compared with the results of molecular modeling using the known 3D structures of KlenTaq polymerase–DNA–dNTP complexes. The dUTPs were C5-modified with bulky functional groups (the Cy5 dye analogs) or lighter aromatic groups. Comparing the experimental data and the results of molecular modeling revealed the decrease in PCR efficiency in the presence of modified dUTPs with an increase in the number of non-covalent bonds between the substituents and the DNA polymerase (about 15% decrease per one extra non-covalent bond). Generalization of the revealed patterns to all the studied polymerases of the A and B families is discussed herein. The number of non-covalent bonds between the substituents and polymerase amino acid residues is proposed to be a potentially variable parameter for regulating enzyme activity. Full article
(This article belongs to the Special Issue Cutting-Edge Research of Nucleic Acid Polymerases)
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