NDLI: Optimized topographical labeling for identification of unknown nucleic acids

Content Provider	IEEE Xplore Digital Library
Author	Miu-Ling Lam Bin Chen Ting-Hsuan Chen
Copyright Year	2015
Description	Author affiliation: Sch. of Creative Media, City Univ. of Hong Kong, Hong Kong, China (Miu-Ling Lam; Bin Chen; Ting-Hsuan Chen)
Abstract	Detection of nucleic acid biomarker has particular importance for disease diagnosis and environmental safety. Yet the identification of low-abundant nucleic acids with unknown sequence remains extremely challenging. Previously we reported a strategy to identify short cDNA molecules using nicking endonucleases that create sequence-specific topographical labels visible by AFM. As such, the identity of the unknown cDNA molecules can be determined based on the labeling patterns composed by the locations of and the spacing between the labels. Here, in order to improve the accuracy, we optimized all possible combinations from total 8 types of nicking endonucleases. The results showed that, based on an optimized combination, NtBsmAI + NtBstNBI + NtAlwI, the average accuracy was improved to 97.1 ± 5.6% as compared with the average accuracy of 51.2 ± 34.4% where only one type of nicking endonuclease was used. More importantly, this improved accuracy is applicable to more than over 85% of human mRNA transcripts. Together, our study suggests an optimization strategy for detecting nucleic acid with unknown sequence using AFM-based measurement, with applications for identifying pathogen and disease at single molecule level.
Sponsorship	IEEE Nanotechnol. Council
Starting Page	205
Ending Page	208
File Size	794015
Page Count	4
File Format	PDF
ISBN	9781467366953
DOI	10.1109/NEMS.2015.7147411
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-04-07
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Accuracy Labeling DNA Diseases Biochemistry Databases Libraries Bioinformatics Nucleic Acids AFM
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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