Current and Emerging Methods for the Synthesis of Single-Stranded DNA

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2020 Jan 25

PMID 31973021

Citations 14

Authors

Min Hao

Jianjun Qiao

Hao Qi

Affiliations

Soon will be listed here.

Abstract

Methods for synthesizing arbitrary single-strand DNA (ssDNA) fragments are rapidly becoming fundamental tools for gene editing, DNA origami, DNA storage, and other applications. To meet the rising application requirements, numerous methods have been developed to produce ssDNA. Some approaches allow the synthesis of freely chosen user-defined ssDNA sequences to overcome the restrictions and limitations of different length, purity, and yield. In this perspective, we provide an overview of the representative ssDNA production strategies and their most significant challenges to enable the readers to make informed choices of synthesis methods and enhance the availability of increasingly inexpensive synthetic ssDNA. We also aim to stimulate a broader interest in the continued development of efficient ssDNA synthesis techniques and improve their applications in future research.

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References

Veneziano R, Ratanalert S, Zhang K, Zhang F, Yan H, Chiu W . Designer nanoscale DNA assemblies programmed from the top down. Science. 2016; 352(6293):1534. PMC: 5111087. DOI: 10.1126/science.aaf4388. View

Marimuthu C, Tang T, Tominaga J, Tan S, Gopinath S . Single-stranded DNA (ssDNA) production in DNA aptamer generation. Analyst. 2012; 137(6):1307-15. DOI: 10.1039/c2an15905h. View

Liu H, Li L, Duan L, Wang X, Xie Y, Tong L . High specific and ultrasensitive isothermal detection of microRNA by padlock probe-based exponential rolling circle amplification. Anal Chem. 2013; 85(16):7941-7. DOI: 10.1021/ac401715k. View

Kwasnieski J, Mogno I, Myers C, Corbo J, Cohen B . Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci U S A. 2012; 109(47):19498-503. PMC: 3511131. DOI: 10.1073/pnas.1210678109. View

Miura H, Gurumurthy C, Sato T, Sato M, Ohtsuka M . CRISPR/Cas9-based generation of knockdown mice by intronic insertion of artificial microRNA using longer single-stranded DNA. Sci Rep. 2015; 5:12799. PMC: 4525291. DOI: 10.1038/srep12799. View

Pease A, Solas D, SULLIVAN E, Cronin M, Holmes C, Fodor S . Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A. 1994; 91(11):5022-6. PMC: 43922. DOI: 10.1073/pnas.91.11.5022. View

Kishi J, Schaus T, Gopalkrishnan N, Xuan F, Yin P . Programmable autonomous synthesis of single-stranded DNA. Nat Chem. 2018; 10(2):155-164. PMC: 5784857. DOI: 10.1038/nchem.2872. View

Huang R, He L, Li S, Liu H, Jin L, Chen Z . A simple fluorescence aptasensor for gastric cancer exosome detection based on branched rolling circle amplification. Nanoscale. 2020; 12(4):2445-2451. DOI: 10.1039/c9nr08747h. View

Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N . Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000; 28(12):E63. PMC: 102748. DOI: 10.1093/nar/28.12.e63. View

10.

Fodor S, Read J, Pirrung M, Stryer L, Lu A, Solas D . Light-directed, spatially addressable parallel chemical synthesis. Science. 1991; 251(4995):767-73. DOI: 10.1126/science.1990438. View

11.

Ding J, Gan S, Ho B . Single-stranded DNA oligoaptamers: molecular recognition and LPS antagonism are length- and secondary structure-dependent. J Innate Immun. 2010; 1(1):46-58. PMC: 7312852. DOI: 10.1159/000145542. View

12.

Lee H, Kalhor R, Goela N, Bolot J, Church G . Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nat Commun. 2019; 10(1):2383. PMC: 6546792. DOI: 10.1038/s41467-019-10258-1. View

13.

Demidov V . Rolling-circle amplification in DNA diagnostics: the power of simplicity. Expert Rev Mol Diagn. 2002; 2(6):542-8. DOI: 10.1586/14737159.2.6.542. View

14.

Bruand C, Ehrlich S . UvrD-dependent replication of rolling-circle plasmids in Escherichia coli. Mol Microbiol. 2000; 35(1):204-10. DOI: 10.1046/j.1365-2958.2000.01700.x. View

15.

Wan W, Li L, Xu Q, Wang Z, Yao Y, Wang R . Error removal in microchip-synthesized DNA using immobilized MutS. Nucleic Acids Res. 2014; 42(12):e102. PMC: 4081059. DOI: 10.1093/nar/gku405. View

16.

Jensen M, Davis R . Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges. Biochemistry. 2018; 57(12):1821-1832. PMC: 7995564. DOI: 10.1021/acs.biochem.7b00937. View

17.

Heiat M, Ranjbar R, Latifi A, Rasaee M, Farnoosh G . Essential strategies to optimize asymmetric PCR conditions as a reliable method to generate large amount of ssDNA aptamers. Biotechnol Appl Biochem. 2016; 64(4):541-548. DOI: 10.1002/bab.1507. View

18.

Zhou B, Dong Q, Ma R, Chen Y, Yang J, Sun L . Rapid isolation of highly pure single-stranded DNA from phagemids. Anal Biochem. 2009; 389(2):177-9. PMC: 2692612. DOI: 10.1016/j.ab.2009.03.044. View

19.

Meiser L, Antkowiak P, Koch J, Chen W, Kohll A, Stark W . Reading and writing digital data in DNA. Nat Protoc. 2019; 15(1):86-101. DOI: 10.1038/s41596-019-0244-5. View

20.

Holmberg A, Blomstergren A, Nord O, Lukacs M, Lundeberg J, Uhlen M . The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures. Electrophoresis. 2005; 26(3):501-10. DOI: 10.1002/elps.200410070. View