Literature DB >> 27294440

Nucleic Acid-Based Nanodevices in Biological Imaging.

Kasturi Chakraborty1, Aneesh T Veetil1, Samie R Jaffrey2, Yamuna Krishnan1,3.   

Abstract

The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.

Entities:  

Keywords:  AFM; FISH; Spinach; aptamers; functional bioimaging; live imaging; nucleic acid nanodevices; structural DNA nanotechnology; super-resolution microscopy

Mesh:

Substances:

Year:  2016        PMID: 27294440      PMCID: PMC5522603          DOI: 10.1146/annurev-biochem-060815-014244

Source DB:  PubMed          Journal:  Annu Rev Biochem        ISSN: 0066-4154            Impact factor:   23.643


  154 in total

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Journal:  Diagn Mol Pathol       Date:  2003-03

2.  Dynamics of single mRNPs in nuclei of living cells.

Authors:  Yaron Shav-Tal; Xavier Darzacq; Shailesh M Shenoy; Dahlene Fusco; Susan M Janicki; David L Spector; Robert H Singer
Journal:  Science       Date:  2004-06-18       Impact factor: 47.728

3.  MicroRNA expression in zebrafish embryonic development.

Authors:  Erno Wienholds; Wigard P Kloosterman; Eric Miska; Ezequiel Alvarez-Saavedra; Eugene Berezikov; Ewart de Bruijn; H Robert Horvitz; Sakari Kauppinen; Ronald H A Plasterk
Journal:  Science       Date:  2005-05-26       Impact factor: 47.728

4.  Conformational transitions as determinants of specificity for the DNA methyltransferase EcoRI.

Authors:  Ben Youngblood; Norbert O Reich
Journal:  J Biol Chem       Date:  2006-07-15       Impact factor: 5.157

5.  Polyfluorophores on a DNA backbone: a multicolor set of labels excited at one wavelength.

Authors:  Yin Nah Teo; James N Wilson; Eric T Kool
Journal:  J Am Chem Soc       Date:  2009-03-25       Impact factor: 15.419

6.  Fluorescence and super-resolution standards based on DNA origami.

Authors:  Jürgen J Schmied; Andreas Gietl; Phil Holzmeister; Carsten Forthmann; Christian Steinhauer; Thorben Dammeyer; Philip Tinnefeld
Journal:  Nat Methods       Date:  2012-12       Impact factor: 28.547

7.  Molecular hybridization of radioactive DNA to the DNA of cytological preparations.

Authors:  M L Pardue; J G Gall
Journal:  Proc Natl Acad Sci U S A       Date:  1969-10       Impact factor: 11.205

8.  Aptamer:toxin conjugates that specifically target prostate tumor cells.

Authors:  Ted C Chu; John W Marks; Laura A Lavery; Sarah Faulkner; Michael G Rosenblum; Andrew D Ellington; Matthew Levy
Journal:  Cancer Res       Date:  2006-06-15       Impact factor: 12.701

9.  A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells.

Authors:  Sonali Saha; Ved Prakash; Saheli Halder; Kasturi Chakraborty; Yamuna Krishnan
Journal:  Nat Nanotechnol       Date:  2015-06-22       Impact factor: 39.213

Review 10.  Fluorescent probes for live-cell RNA detection.

Authors:  Gang Bao; Won Jong Rhee; Andrew Tsourkas
Journal:  Annu Rev Biomed Eng       Date:  2009       Impact factor: 9.590

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  37 in total

1.  A DNA nanomachine chemically resolves lysosomes in live cells.

Authors:  KaHo Leung; Kasturi Chakraborty; Anand Saminathan; Yamuna Krishnan
Journal:  Nat Nanotechnol       Date:  2018-12-03       Impact factor: 39.213

2.  DNA-based fluorescent probes of NOS2 activity in live brains.

Authors:  Aneesh T Veetil; Junyi Zou; Katharine W Henderson; Maulik S Jani; Shabana M Shaik; Sangram S Sisodia; Melina E Hale; Yamuna Krishnan
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-17       Impact factor: 11.205

3.  Split T7 RNA polymerase biosensors to study multiprotein interaction dynamics.

Authors:  Jeffrey A Dewey; Bryan C Dickinson
Journal:  Methods Enzymol       Date:  2020-06-15       Impact factor: 1.600

4.  DNA nanodevices map enzymatic activity in organelles.

Authors:  Krishna Dan; Aneesh T Veetil; Kasturi Chakraborty; Yamuna Krishnan
Journal:  Nat Nanotechnol       Date:  2019-02-11       Impact factor: 39.213

5.  Nano on reflection.

Authors: 
Journal:  Nat Nanotechnol       Date:  2016-10-05       Impact factor: 39.213

Review 6.  RNA Localization in Bacteria.

Authors:  Jingyi Fei; Cynthia M Sharma
Journal:  Microbiol Spectr       Date:  2018-09

7.  Portable platform for rapid in-field identification of human fecal pollution in water.

Authors:  Yu Sherry Jiang; Timothy E Riedel; Jessica A Popoola; Barrett R Morrow; Sheng Cai; Andrew D Ellington; Sanchita Bhadra
Journal:  Water Res       Date:  2017-12-13       Impact factor: 11.236

Review 8.  Recent Developments in Nanosensors for Imaging Applications in Biological Systems.

Authors:  Guoxin Rong; Erin E Tuttle; Ashlyn Neal Reilly; Heather A Clark
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2019-03-11       Impact factor: 10.745

9.  Protein Spherical Nucleic Acids for Live-Cell Chemical Analysis.

Authors:  Devleena Samanta; Sasha B Ebrahimi; Caroline D Kusmierz; Ho Fung Cheng; Chad A Mirkin
Journal:  J Am Chem Soc       Date:  2020-07-24       Impact factor: 15.419

10.  A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition.

Authors:  Suruchi Sharma; Matthew Zajac; Yamuna Krishnan
Journal:  Chembiochem       Date:  2019-08-29       Impact factor: 3.164

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