A device for automated hydrodynamic shearing of genomic DNA

BioTechniques

Volumn 46, Issue 7, 2009, Pages 553-556

  Joneja, Aric ^a   Huang, Xiaohua ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

DNA shearing; Filter screen; Genome sequencing; Genomic DNA fragmentation; Genomic DNA libraries; Hydrodynamic shear stress

Indexed keywords

DNA FRAGMENT; DNA;

CONTAMINATION; DEVICE; DISPOSABLE EQUIPMENT; DNA FRAGMENTATION; FLOW RATE; FLUID FLOW; FRAGMENTATION REACTION; GENOMICS; HEARING AID; HUMAN; HYDRODYNAMICS; REPRODUCIBILITY; SCREENING; SHORT SURVEY; ARTICLE; AUTOMATION; GENETICS; HUMAN GENOME; INSTRUMENTATION; MICROFLUIDICS; POROSITY;

AUTOMATION; DNA; GENOME, HUMAN; HUMANS; MICROFLUIDICS; POROSITY; REPRODUCIBILITY OF RESULTS;

EID: 70349258335     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/000113123     Document Type: Short Survey

References (16)

1. Anderson, S. 1981. Shotgun DNA sequencing using cloned DNase I-generated fragments. Nucleic Acids Res. 9:3015-3027.
2. Roe, B.A. 2004. Shotgun l ibrary construction for DNA sequencing. Methods Mol. Biol. 255:171-187.
3. Seed, B., R.C. Parker, and N. Davidson. 1982. Representation of DNA sequences in recombinant DNA libraries prepared by restriction enzyme partial digestion. Gene 19:201-209. (Pubitemid 13203248)
4. Gingrich, J.C., D.M. Boehrer, and S.B. Basu. 1996. Partial CviJI digestion as an alternative approach to generate cosmid sublibraries for large-scale sequencing projects. BioTechniques 21:99-104.
5. Hoheisel, J.D., D. Nizetic, and H. Lehrach. 1989. Control of partial digestion combining the enzymes dam methylase and MboI. Nucleic Acids Res. 17:9571-9582.
6. Wong, K.K., L.M. Markillie, and J.D. Saffer. 1997. A novel method for producing partial restriction digestion of DNA fragments by PCR with 5-methyl-CTP. Nucleic Acids Res. 25:4169-4171.
7. Osoegawa, K., A.G. Mammoser, C. Wu, E. Frengen, C. Zeng, J.J. Catanese, and P.J. de Jong. 2001. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 11:483-496. (Pubitemid 32243858)
8. Deininger, P.L. 1983. Approaches to rapid DNA sequence analysis. Anal. Biochem. 135:247-263.
9. Okpodu, C.M., D. Robertson, W.F. Boss, R.K. Togasaki, and S.J. Surzycki. 1994. Rapid isolation of nuclei from carrot suspension culture cells using a BioNebulizer. BioTechniques 16:154-159. (Pubitemid 2033241)
10. Hengen, P.N. 1997. Shearing DNA for genomic library construction. Trends Biochem. Sci. 22:273-274.
11. Burger, G., D.V. Lavrov, L. Forget, and B.F. Lang. 2007. Sequencing complete mitochondrial and plastid genomes. Nat. Protocols 2:603-614. (Pubitemid 47044695)
12. Oefner, P.J., S.P. Hunicke-Smith, L. Chiang, F. Dietrich, J. Mulligan, and R.W. Davis. 1996. Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. Nucleic Acids Res. 24:3879-3886.
13. Thorstenson, Y.R., S.P. Hunicke-Smith, P.J. Oefner, and R.W. Davis. 1998. An automated hydrodynamic process for controlled, unbiased DNA shearing. Genome Res. 8:848-855.
14. Bertazzoni, U. 1975. Analysis of the breaking sites in the physical degradation of DNA. Biochim. Biophys. Acta 395:239-245.
15. McKee, J.R., C.L. Christman, W.D. O'Brien, Jr., and S.Y. Wang. 1977. Effects of ultrasound on nucleic acid bases. Biochemistry 16:4651-4654. (Pubitemid 8205602)
16. Roe, B.A., J.S. Crabtree, and A.S. Khan. 1996. DNA Isolation and Sequencing. John Wiley & Sons, New York.