Literature DB >> 32144741

Recent progress of in-cell NMR of nucleic acids in living human cells.

Yudai Yamaoki1, Takashi Nagata1,2, Tomoki Sakamoto2, Masato Katahira3,4.   

Abstract

The inside of living cells is highly crowded with biological macromolecules. It has long been considered that the properties of nucleic acids and proteins, such as their structures, dynamics, interactions, and enzymatic activities, in intracellular environments are different from those under in vitro dilute conditions. In-cell NMR is a robust and powerful method used in the direct measurement of those properties in living cells. However, until 2 years ago, in-cell NMR was limited to Xenopus laevis oocytes due to technical challenges of incorporating exogenous nucleic acids. In the last 2 years, in-cell NMR spectra of nucleic acid introduced into living human cells have been reported. By use of the in-cell NMR spectra of nucleic acids in living human cells, the formation of hairpin structures with Watson-Crick base pairs, and i-motif and G-quadruplex structures with non-Watson-Crick base pairs was demonstrated. Others investigated the mRNA-antisense drug interactions and DNA-small compound interactions. In this article, we review these studies to underscore the potential of in-cell NMR for addressing the structures, dynamics, and interactions of nucleic acids in living human cells.

Entities:  

Keywords:  DNA; Human cell; In-cell NMR; Intracellular structure; RNA; Streptolysin O (SLO)

Year:  2020        PMID: 32144741      PMCID: PMC7242591          DOI: 10.1007/s12551-020-00664-x

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  43 in total

1.  Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes.

Authors:  Philipp Selenko; Zach Serber; Bedrick Gadea; Joan Ruderman; Gerhard Wagner
Journal:  Proc Natl Acad Sci U S A       Date:  2006-07-27       Impact factor: 11.205

2.  SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds.

Authors:  Paul Schanda; Eriks Kupce; Bernhard Brutscher
Journal:  J Biomol NMR       Date:  2005-12       Impact factor: 2.835

3.  The cell resealing technique for manipulating, visualizing, and elucidating molecular functions in living cells.

Authors:  Rina Kunishige; Fumi Kano; Masayuki Murata
Journal:  Biochim Biophys Acta Gen Subj       Date:  2019-03-23       Impact factor: 3.770

4.  In situ structural biology using in-cell NMR.

Authors:  Noritaka Nishida; Yutaka Ito; Ichio Shimada
Journal:  Biochim Biophys Acta Gen Subj       Date:  2019-05-16       Impact factor: 3.770

Review 5.  Characterization of noncoding regulatory DNA in the human genome.

Authors:  Ran Elkon; Reuven Agami
Journal:  Nat Biotechnol       Date:  2017-08-08       Impact factor: 54.908

Review 6.  Soft interactions and crowding.

Authors:  Mohona Sarkar; Conggang Li; Gary J Pielak
Journal:  Biophys Rev       Date:  2013-02-21

7.  Balanced Regulation of Redox Status of Intracellular Thioredoxin Revealed by in-Cell NMR.

Authors:  Ayano Mochizuki; Arata Saso; Qingci Zhao; Satoshi Kubo; Noritaka Nishida; Ichio Shimada
Journal:  J Am Chem Soc       Date:  2018-03-06       Impact factor: 15.419

8.  Structure of proteins in eukaryotic compartments.

Authors:  Karl Bertrand; Sergey Reverdatto; David S Burz; Richard Zitomer; Alexander Shekhtman
Journal:  J Am Chem Soc       Date:  2012-07-19       Impact factor: 15.419

9.  Analysis of Interactions between Telomeric i-Motif DNA and a Cyclic Tetraoxazole Compound.

Authors:  Shadi Sedghi Masoud; Yudai Yamaoki; Yue Ma; Adrien Marchand; Fernaldo Richtia Winnerdy; Valérie Gabelica; Anh Tuân Phan; Masato Katahira; Kazuo Nagasawa
Journal:  Chembiochem       Date:  2018-10-12       Impact factor: 3.164

10.  A Dual-App Nucleoside Probe Provides Structural Insights into the Human Telomeric Overhang in Live Cells.

Authors:  Sudeshna Manna; Debayan Sarkar; Seergazhi G Srivatsan
Journal:  J Am Chem Soc       Date:  2018-09-21       Impact factor: 15.419

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  4 in total

1.  Biophysical Reviews' national biophysical society partnership program.

Authors:  Damien Hall
Journal:  Biophys Rev       Date:  2020-04-29

2.  Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy.

Authors:  Daniel Krafčík; Eva Ištvánková; Šimon Džatko; Pavlína Víšková; Silvie Foldynová-Trantírková; Lukáš Trantírek
Journal:  Int J Mol Sci       Date:  2021-06-03       Impact factor: 5.923

Review 3.  Utilizing magnetic resonance techniques to study membrane interactions of amyloid peptides.

Authors:  Sunnia Rajput; Marc-Antoine Sani; David W Keizer; Frances Separovic
Journal:  Biochem Soc Trans       Date:  2021-06-30       Impact factor: 5.407

4.  In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells.

Authors:  P Broft; S Dzatko; M Krafcikova; A Wacker; Robert Hänsel-Hertsch; Volker Dötsch; L Trantirek; Harald Schwalbe
Journal:  Angew Chem Int Ed Engl       Date:  2020-11-09       Impact factor: 16.823

  4 in total

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