Next Article in Journal
Spatial Regulation of Epidermal Growth Factor Receptor Signaling by Endocytosis
Previous Article in Journal
Immunological Effects of Oenothein B, an Ellagitannin Dimer, on Dendritic Cells
Int. J. Mol. Sci. 2013, 14(1), 57-71; doi:10.3390/ijms14010057
Article

Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization

1,2,* , 2
,
2
,
2
,
2,3
,
4
,
5
,
2
 and
6,7
1 Department of Molecular and Cell Biology, University of California, Berkeley (UCB), Berkeley, CA 94720, USA 2 Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA 3 Department of Pathology, University of California, San Francisco (UCSF), CA 94143, USA 4 Department of Diabetes, City of Hope, 1500 Duarte Road, Duarte, CA 91010-3012, USA 5 Department of Fetal Medicine, Whipps Cross University Hospital, Barts Health NHS Trust, London E11 1NR, UK 6 William Harvey Research Institute, Queen Mary University London, Barts Health London, London EC1A 7BE, UK 7 Department of Anesthesiology, German Heart Institute, Berlin 13353, Germany
* Author to whom correspondence should be addressed.
Received: 2 December 2012 / Revised: 9 December 2012 / Accepted: 10 December 2012 / Published: 20 December 2012
(This article belongs to the Section Molecular Pathology)
View Full-Text   |   Download PDF [1327 KB, uploaded 19 June 2014]   |   Browse Figures

Abstract

Chromosome enumeration in interphase and metaphase cells using fluorescence in situ hybridization (FISH) is an established procedure for the rapid and accurate cytogenetic analysis of cell nuclei and polar bodies, the unambiguous gender determination, as well as the definition of tumor-specific signatures. Present bottlenecks in the procedure are a limited number of commercial, non-isotopically labeled probes that can be combined in multiplex FISH assays and the relatively high price and effort to develop additional probes. We describe a streamlined approach for rapid probe definition, synthesis and validation, which is based on the analysis of publicly available DNA sequence information, also known as “database mining”. Examples of probe preparation for the human gonosomes and chromosome 16 as a selected autosome outline the probe selection strategy, define a timeline for expedited probe production and compare this novel selection strategy to more conventional probe cloning protocols.
Keywords: molecular cytogenetics; chromosomes; heterochromatin; DNA repeats; data mining; fluorescence in situ hybridization; bacterial artificial chromosomes; DNA probes molecular cytogenetics; chromosomes; heterochromatin; DNA repeats; data mining; fluorescence in situ hybridization; bacterial artificial chromosomes; DNA probes
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Share & Cite This Article

Further Mendeley | CiteULike
Export to BibTeX |
EndNote
MDPI and ACS Style

Hsu, J.H.; Zeng, H.; Lemke, K.H.; Polyzos, A.A.; Weier, J.F.; Wang, M.; Lawin-O'Brien, A.R.; Weier, H.-U.G.; O'Brien, B. Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization. Int. J. Mol. Sci. 2013, 14, 57-71.

View more citation formats

Related Articles

Article Metrics

For more information on the journal, click here

Comments

Cited By

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert