DNA Barcodes for Rapid, Whole Genome, Single-molecule Analyses

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Mar 29

PMID 30918971

Citations 10

Authors

Nathaniel O Wand

Darren A Smith

Andrew A Wilkinson

Ashleigh E Rushton

Stephen J W Busby

Iain B Styles

Robert K Neely

Affiliations

Soon will be listed here.

Abstract

We report an approach for visualizing DNA sequence and using these 'DNA barcodes' to search complex mixtures of genomic material for DNA molecules of interest. We demonstrate three applications of this methodology; identifying specific molecules of interest from a dataset containing gigabasepairs of genome; identification of a bacterium from such a dataset and, finally, by locating infecting virus molecules in a background of human genomic material. As a result of the dense fluorescent labelling of the DNA, individual barcodes of the order 40 kb pairs in length can be reliably identified. This means DNA can be prepared for imaging using standard handling and purification techniques. The recorded dataset provides stable physical and electronic records of the total genomic content of a sample that can be readily searched for a molecule or region of interest.

Citing Articles

OM2Seq: learning retrieval embeddings for optical genome mapping.

Nogin Y, Sapir D, Zur T, Weinberger N, Belinkov Y, Ebenstein Y Bioinform Adv. 2024; 4(1):vbae079.

PMID: 38915884 PMC: 11194751. DOI: 10.1093/bioadv/vbae079.

Design of optimal labeling patterns for optical genome mapping via information theory.

Nogin Y, Bar-Lev D, Hanania D, Zur T, Ebenstein Y, Yaakobi E Bioinformatics. 2023; 39(10).

PMID: 37758248 PMC: 10563147. DOI: 10.1093/bioinformatics/btad601.

DeepOM: single-molecule optical genome mapping via deep learning.

Nogin Y, Zur T, Margalit S, Barzilai I, Alalouf O, Ebenstein Y Bioinformatics. 2023; 39(3).

PMID: 36929928 PMC: 10049785. DOI: 10.1093/bioinformatics/btad137.

DNA Labeling Using DNA Methyltransferases.

Tomkuviene M, Kriukiene E, Klimasauskas S Adv Exp Med Biol. 2022; 1389:535-562.

PMID: 36350522 DOI: 10.1007/978-3-031-11454-0_19.

A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy.

Goyal G, Ekedahl E, Nyblom M, Krog J, Frobrant E, Brander M Sci Rep. 2022; 12(1):9301.

PMID: 35660772 PMC: 9166776. DOI: 10.1038/s41598-022-13315-w.

References

Forde B, Ben Zakour N, Stanton-Cook M, Phan M, Totsika M, Peters K . The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One. 2014; 9(8):e104400. PMC: 4134206. DOI: 10.1371/journal.pone.0104400. View

Deen J, Sempels W, De Dier R, Vermant J, Dedecker P, Hofkens J . Combing of genomic DNA from droplets containing picograms of material. ACS Nano. 2015; 9(1):809-16. PMC: 4344373. DOI: 10.1021/nn5063497. View

Deen J, Wang S, Van Snick S, Leen V, Janssen K, Hofkens J . A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA. Nucleic Acids Res. 2018; 46(11):e64. PMC: 6009647. DOI: 10.1093/nar/gky184. View

Kronenberg Z, Fiddes I, Gordon D, Murali S, Cantsilieris S, Meyerson O . High-resolution comparative analysis of great ape genomes. Science. 2018; 360(6393). PMC: 6178954. DOI: 10.1126/science.aar6343. View

Edelstein A, Tsuchida M, Amodaj N, Pinkard H, Vale R, Stuurman N . Advanced methods of microscope control using μManager software. J Biol Methods. 2015; 1(2). PMC: 4297649. DOI: 10.14440/jbm.2014.36. View

Helmer Lauer M, Vranken C, Deen J, Frederickx W, Vanderlinden W, Wand N . Methyltransferase-directed covalent coupling of fluorophores to DNA. Chem Sci. 2017; 8(5):3804-3811. PMC: 5436541. DOI: 10.1039/c6sc04229e. View

Bianco J, Poli J, Saksouk J, Bacal J, Silva M, Yoshida K . Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing. Methods. 2012; 57(2):149-57. DOI: 10.1016/j.ymeth.2012.04.007. View

Levy-Sakin M, Grunwald A, Kim S, Gassman N, Gottfried A, Antelman J . Toward single-molecule optical mapping of the epigenome. ACS Nano. 2013; 8(1):14-26. PMC: 4022788. DOI: 10.1021/nn4050694. View

Pendleton M, Sebra R, Pang A, Ummat A, Franzen O, Rausch T . Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods. 2015; 12(8):780-6. PMC: 4646949. DOI: 10.1038/nmeth.3454. View

10.

Jain M, Koren S, Miga K, Quick J, Rand A, Sasani T . Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018; 36(4):338-345. PMC: 5889714. DOI: 10.1038/nbt.4060. View

11.

Mak A, Lai Y, Lam E, Kwok T, Leung A, Poon A . Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays. Genetics. 2015; 202(1):351-62. PMC: 4701098. DOI: 10.1534/genetics.115.183483. View

12.

Kaykov A, Taillefumier T, Bensimon A, Nurse P . Molecular Combing of Single DNA Molecules on the 10 Megabase Scale. Sci Rep. 2016; 6:19636. PMC: 4726065. DOI: 10.1038/srep19636. View

13.

Teague B, Waterman M, Goldstein S, Potamousis K, Zhou S, Reslewic S . High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A. 2010; 107(24):10848-53. PMC: 2890719. DOI: 10.1073/pnas.0914638107. View

14.

Muller V, Westerlund F . Optical DNA mapping in nanofluidic devices: principles and applications. Lab Chip. 2017; 17(4):579-590. DOI: 10.1039/c6lc01439a. View

15.

Deschamps S, Zhang Y, Llaca V, Ye L, Sanyal A, King M . A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping. Nat Commun. 2018; 9(1):4844. PMC: 6242865. DOI: 10.1038/s41467-018-07271-1. View

16.

Zirkin S, Fishman S, Sharim H, Michaeli Y, Don J, Ebenstein Y . Lighting up individual DNA damage sites by in vitro repair synthesis. J Am Chem Soc. 2014; 136(21):7771-6. DOI: 10.1021/ja503677n. View

17.

Kim S, Gottfried A, Lin R, Dertinger T, Kim A, Chung S . Enzymatically incorporated genomic tags for optical mapping of DNA-binding proteins. Angew Chem Int Ed Engl. 2012; 51(15):3578-81. PMC: 3417104. DOI: 10.1002/anie.201107714. View

18.

Neely R, Deen J, Hofkens J . Optical mapping of DNA: single-molecule-based methods for mapping genomes. Biopolymers. 2011; 95(5):298-311. DOI: 10.1002/bip.21579. View

19.

Lacroix J, Pelofy S, Blatche C, Pillaire M, Huet S, Chapuis C . Analysis of DNA Replication by Optical Mapping in Nanochannels. Small. 2016; 12(43):5963-5970. DOI: 10.1002/smll.201503795. View

20.

Iyer D, Das S, Rhind N . Analysis of DNA Replication in Fission Yeast by Combing. Cold Spring Harb Protoc. 2017; 2018(3). DOI: 10.1101/pdb.prot092015. View