publications

2023

1. Machine learning directed aptamer search from conserved primary sequences and secondary structures

   Javier Perez Tobia, Po-Jung Jimmy Huang, Yuzhe Ding, Runjhun Saran Narayan, Apurva Narayan, and 1 more author

   ACS Synthetic Biology, 2023

   Bib PDF Code

   @article{perez2023machine,
     title = {Machine learning directed aptamer search from conserved primary sequences and secondary structures},
     author = {Perez Tobia, Javier and Huang, Po-Jung Jimmy and Ding, Yuzhe and Saran Narayan, Runjhun and Narayan, Apurva and Liu, Juewen},
     journal = {ACS Synthetic Biology},
     volume = {12},
     number = {1},
     pages = {186--195},
     year = {2023},
     publisher = {American Chemical Society},
     bibtex_show = true,
     selected = true
   }

2. cAPTured: Neural Reflex Arc-Inspired Fuzzy Continual Learning for Capturing in Silico Aptamer-Target Protein Interactions

   Aviral Chharia, Runjhun Saran, and Apurva Narayan

   In 2023 International Joint Conference on Neural Networks (IJCNN), 2023

   Bib PDF Code

   @inproceedings{chharia2023captured,
     title = {cAPTured: Neural Reflex Arc-Inspired Fuzzy Continual Learning for Capturing in Silico Aptamer-Target Protein Interactions},
     author = {Chharia, Aviral and Saran, Runjhun and Narayan, Apurva},
     booktitle = {2023 International Joint Conference on Neural Networks (IJCNN)},
     pages = {1--9},
     year = {2023},
     organization = {IEEE},
     bibtex_show = true,
   }

2021

1. Phosphorothioate nucleic acids for probing metal binding, biosensing and nanotechnology

   Runjhun Saran, Zhicheng Huang, and Juewen Liu

   Coordination Chemistry Reviews, 2021

   Bib PDF

   @article{saran2021phosphorothioate,
     title = {Phosphorothioate nucleic acids for probing metal binding, biosensing and nanotechnology},
     author = {Saran, Runjhun and Huang, Zhicheng and Liu, Juewen},
     journal = {Coordination Chemistry Reviews},
     volume = {428},
     pages = {213624},
     year = {2021},
     publisher = {Elsevier},
     bibtex_show = true,
   }

2. Thioflavin T fluorescence and NMR spectroscopy suggesting a non-G-quadruplex structure for a sodium binding aptamer embedded in DNAzymes

   Runjhun Saran, Kyle A Piccolo, Yanping He, Yongqiang Kang, Po-Jung Jimmy Huang, and 4 more authors

   Canadian Journal of Chemistry, 2021

   Bib PDF

   @article{saran2021thioflavin,
     title = {Thioflavin T fluorescence and NMR spectroscopy suggesting a non-G-quadruplex structure for a sodium binding aptamer embedded in DNAzymes},
     author = {Saran, Runjhun and Piccolo, Kyle A and He, Yanping and Kang, Yongqiang and Huang, Po-Jung Jimmy and Wei, Chunying and Chen, Da and Dieckmann, Thorsten and Liu, Juewen},
     journal = {Canadian Journal of Chemistry},
     volume = {99},
     number = {11},
     pages = {860--866},
     year = {2021},
     publisher = {NRC Research Press 1840 Woodward Drive, Suite 1, Ottawa, ON K2C 0P7},
     bibtex_show = true,
   }

2020

1. Mechanical flexibility of DNA: a quintessential tool for DNA nanotechnology

   Runjhun Saran, Yong Wang, and Isaac TS Li

   Sensors, 2020

   Bib PDF

   @article{saran2020mechanical,
     title = {Mechanical flexibility of DNA: a quintessential tool for DNA nanotechnology},
     author = {Saran, Runjhun and Wang, Yong and Li, Isaac TS},
     journal = {Sensors},
     volume = {20},
     number = {24},
     pages = {7019},
     year = {2020},
     publisher = {MDPI},
     bibtex_show = true,
   }

2018

1. Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence

   Runjhun Saran, Lu Yao, Peter Hoang, and Juewen Liu

   Biochimie, 2018

   Bib PDF

   @article{saran2018folding,
     title = {Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence},
     author = {Saran, Runjhun and Yao, Lu and Hoang, Peter and Liu, Juewen},
     journal = {Biochimie},
     volume = {145},
     pages = {145--150},
     year = {2018},
     publisher = {Elsevier},
     bibtex_show = true,
   }

2. Reselection yielding a smaller and more active silver-specific DNAzyme

   Lide Gu, Runjhun Saran, Wanli Yan, Po-Jung Jimmy Huang, Shujun Wang, and 2 more authors

   ACS omega, 2018

   Bib PDF

   @article{gu2018reselection,
     title = {Reselection yielding a smaller and more active silver-specific DNAzyme},
     author = {Gu, Lide and Saran, Runjhun and Yan, Wanli and Huang, Po-Jung Jimmy and Wang, Shujun and Lyu, Mingsheng and Liu, Juewen},
     journal = {ACS omega},
     volume = {3},
     number = {11},
     pages = {15174--15181},
     year = {2018},
     publisher = {American Chemical Society},
     bibtex_show = true,
   }

2017

1. A silver-specific DNAzyme with a new silver aptamer and salt-promoted activity

   Runjhun Saran, Kimberly Kleinke, Wenhu Zhou, Tianmeng Yu, and Juewen Liu

   Biochemistry, 2017

   Bib PDF

   @article{saran2017silver,
     title = {A silver-specific DNAzyme with a new silver aptamer and salt-promoted activity},
     author = {Saran, Runjhun and Kleinke, Kimberly and Zhou, Wenhu and Yu, Tianmeng and Liu, Juewen},
     journal = {Biochemistry},
     volume = {56},
     number = {14},
     pages = {1955--1962},
     year = {2017},
     publisher = {ACS Publications},
     bibtex_show = true,
   }

2. Metal sensing by DNA

   Wenhu Zhou, Runjhun Saran, and Juewen Liu

   Chemical reviews, 2017

   Bib PDF

   @article{zhou2017metal,
     title = {Metal sensing by DNA},
     author = {Zhou, Wenhu and Saran, Runjhun and Liu, Juewen},
     journal = {Chemical reviews},
     volume = {117},
     number = {12},
     pages = {8272--8325},
     year = {2017},
     publisher = {American Chemical Society},
     bibtex_show = true,
   }

3. Two completely different mechanisms for highly specific Na+ recognition by DNAzymes

   Wenhu Zhou, Runjhun Saran, Jinsong Ding, and Juewen Liu

   ChemBioChem, 2017

   Bib PDF

   @article{zhou2017two,
     title = {Two completely different mechanisms for highly specific Na+ recognition by DNAzymes},
     author = {Zhou, Wenhu and Saran, Runjhun and Ding, Jinsong and Liu, Juewen},
     journal = {ChemBioChem},
     volume = {18},
     number = {18},
     pages = {1828--1835},
     year = {2017},
     publisher = {Wiley Online Library},
     bibtex_show = true,
   }

4. Back Cover: An Exceptionally Selective DNA Cooperatively Binding Two Ca2+ Ions (ChemBioChem 6/2017)

   Wenhu Zhou, Runjhun Saran, Po-Jung Jimmy Huang, Jinsong Ding, and Juewen Liu

   ChemBioChem, 2017

   Bib PDF

   @article{zhou2017back,
     title = {Back Cover: An Exceptionally Selective DNA Cooperatively Binding Two Ca2+ Ions (ChemBioChem 6/2017)},
     author = {Zhou, Wenhu and Saran, Runjhun and Huang, Po-Jung Jimmy and Ding, Jinsong and Liu, Juewen},
     journal = {ChemBioChem},
     volume = {18},
     number = {6},
     pages = {571--571},
     year = {2017},
     bibtex_show = true,
   }

5. An exceptionally selective DNA cooperatively binding two Ca2+ ions

   Wenhu Zhou, Runjhun Saran, Po-Jung Jimmy Huang, Jinsong Ding, and Juewen Liu

   ChemBioChem, 2017

   Bib PDF

   @article{zhou2017exceptionally,
     title = {An exceptionally selective DNA cooperatively binding two Ca2+ ions},
     author = {Zhou, Wenhu and Saran, Runjhun and Huang, Po-Jung Jimmy and Ding, Jinsong and Liu, Juewen},
     journal = {ChemBioChem},
     volume = {18},
     number = {6},
     pages = {518--522},
     year = {2017},
     bibtex_show = true,
   }

2016

1. Label-free Ag+ detection by enhancing DNA sensitized Tb3+ luminescence

   Kimberly Kleinke, Runjhun Saran, and Juewen Liu

   Sensors, 2016

   Bib

   @article{kleinke2016label,
     title = {Label-free Ag+ detection by enhancing DNA sensitized Tb3+ luminescence},
     author = {Kleinke, Kimberly and Saran, Runjhun and Liu, Juewen},
     journal = {Sensors},
     volume = {16},
     number = {9},
     pages = {1370},
     year = {2016},
     publisher = {MDPI},
     bibtex_show = true
   }

2. A silver DNAzyme

   Runjhun Saran, and Juewen Liu

   Analytical chemistry, 2016

   Bib PDF

   @article{saran2016silver,
     title = {A silver DNAzyme},
     author = {Saran, Runjhun and Liu, Juewen},
     journal = {Analytical chemistry},
     volume = {88},
     number = {7},
     pages = {4014--4020},
     year = {2016},
     publisher = {ACS Publications},
     bibtex_show = true,
   }

3. A new Na+-dependent RNA-cleaving DNAzyme with over 1000-fold rate acceleration by ethanol

   Wenhu Zhou, Runjhun Saran, Qingyun Chen, Jinsong Ding, and Juewen Liu

   ChemBioChem, 2016

   Bib PDF

   @article{zhou2016new,
     title = {A new Na+-dependent RNA-cleaving DNAzyme with over 1000-fold rate acceleration by ethanol},
     author = {Zhou, Wenhu and Saran, Runjhun and Chen, Qingyun and Ding, Jinsong and Liu, Juewen},
     journal = {ChemBioChem},
     volume = {17},
     number = {2},
     pages = {159--163},
     year = {2016},
     bibtex_show = true,
   }

4. A comparison of two classic Pb 2+-dependent RNA-cleaving DNAzymes

   Runjhun Saran, and Juewen Liu

   Inorganic Chemistry Frontiers, 2016

   Bib PDF

   @article{saran2016comparison,
     title = {A comparison of two classic Pb 2+-dependent RNA-cleaving DNAzymes},
     author = {Saran, Runjhun and Liu, Juewen},
     journal = {Inorganic Chemistry Frontiers},
     volume = {3},
     number = {4},
     pages = {494--501},
     year = {2016},
     publisher = {Royal Society of Chemistry},
     bibtex_show = true,
   }

5. Deciphering the role of Atg5 in nucleotide dependent interaction of Rab33B with the dimeric complex, Atg5-Atg16L1

   Mintu Chandra, Runjhun Saran, and Sunando Datta

   Biochemical and biophysical research communications, 2016

   Bib PDF

   @article{chandra2016deciphering,
     title = {Deciphering the role of Atg5 in nucleotide dependent interaction of Rab33B with the dimeric complex, Atg5-Atg16L1},
     author = {Chandra, Mintu and Saran, Runjhun and Datta, Sunando},
     journal = {Biochemical and biophysical research communications},
     volume = {473},
     number = {1},
     pages = {8--16},
     year = {2016},
     publisher = {Elsevier},
     bibtex_show = true,
   }

2015

1. Tandem DNAzymes for mRNA cleavage: Choice of enzyme, metal ions and the antisense effect

   Feng Wang, Runjhun Saran, and Juewen Liu

   Bioorganic & medicinal chemistry letters, 2015

   PDF
2. Searching for a DNAzyme Version of the Leadzyme

   Runjhun Saran, Qingyun Chen, and Juewen Liu

   Journal of molecular evolution, 2015

   Bib PDF

   @article{saran2015searching,
     title = {Searching for a DNAzyme Version of the Leadzyme},
     author = {Saran, Runjhun and Chen, Qingyun and Liu, Juewen},
     journal = {Journal of molecular evolution},
     volume = {81},
     pages = {235--244},
     year = {2015},
     publisher = {Springer US},
     bibtex_show = true,
   }