Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (342K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Albert, T. J.
Right arrow Articles by Green, R. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Albert, T. J.
Right arrow Articles by Green, R. D.
Related Collections
Right arrow Microarray
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 7 e35
© 2003 Oxford University Press

Light-directed 5'->3' synthesis of complex oligonucleotide microarrays

Thomas J. Albert, Jason Norton, Markus Ott1, Todd Richmond, Kate Nuwaysir, Emile F. Nuwaysir, Klaus-Peter Stengele1 and Roland D. Green

NimbleGen Systems Inc., One Science Court, Madison, WI 53711, USA and 1 Chemogenix GmbH, Beuthenerstrasse 2, D-84478 Waldkraiburg, Germany

*To whom correspondence should be addressed. Tel: +1 608 218 7613; Fax: +1 608 218 7601; Email: talbert{at}nimblegen.com

Light-directed synthesis of high-density microarrays is currently performed in the 3'->5' direction due to constraints in existing synthesis chemistry. This results in the probes being unavailable for many common types of enzymatic modification. Arrays that are synthesized in the 5'->3' direction could be utilized to perform parallel genotyping and resequencing directly on the array surface, dramatically increasing the throughput and reducing the cost relative to existing techniques. In this report we demonstrate the use of photoprotected phosphoramidite monomers for light-directed array synthesis in the 5'->3' direction, using maskless array synthesis technology. These arrays have a dynamic range of >2.5 orders of magnitude, sensitivity below 1 pM and a coefficient of variance of <10% across the array surface. Arrays containing >150 000 probe sequences were hybridized to labeled mouse cRNA producing highly concordant data (average R2 = 0.998). We have also shown that the 3' ends of array probes are available for sequence-specific primer extension and ligation reactions.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BloodHome page
J. P. Maciejewski and G. J. Mufti
Whole genome scanning as a cytogenetic tool in hematologic malignancies
Blood, August 15, 2008; 112(4): 965 - 974.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
H. T. Bjornsson, T. J. Albert, C. M. Ladd-Acosta, R. D. Green, M. A. Rongione, C. M. Middle, R. A. Irizarry, K. W. Broman, and A. P. Feinberg
SNP-specific array-based allele-specific expression analysis
Genome Res., May 1, 2008; 18(5): 771 - 779.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. F. Phillips, M. R. Lockett, M. J. Rodesch, M. R. Shortreed, F. Cerrina, and L. M. Smith
In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication
Nucleic Acids Res., January 17, 2008; 36(1): e7 - e7.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
T. T. Liu, S. Znaidi, K. S. Barker, L. Xu, R. Homayouni, S. Saidane, J. Morschhauser, A. Nantel, M. Raymond, and P. D. Rogers
Genome-Wide Expression and Location Analyses of the Candida albicans Tac1p Regulon
Eukaryot. Cell, November 1, 2007; 6(11): 2122 - 2138.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
P. Alvarez, P. Saenz, D. Arteta, A. Martinez, M. Pocovi, L. Simon, and P. Giraldo
Transcriptional Profiling of Hematologic Malignancies with a Low-Density DNA Microarray
Clin. Chem., February 1, 2007; 53(2): 259 - 267.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Kinoshita, K. Fujimoto, T. Yakabe, S. Saito, Y. Hamaguchi, T. Kikuchi, K. Nonaka, S. Murata, D. Masuda, W. Takada, et al.
Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer
Nucleic Acids Res., January 12, 2007; 35(1): e3 - e3.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Li, H. J. Lee, and R. M. Corn
Fabrication and characterization of RNA aptamer microarrays for the study of protein-aptamer interactions with SPR imaging
Nucleic Acids Res., December 2, 2006; 34(22): 6416 - 6424.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Blair, K. Richmond, M. Rodesch, M. Bassetti, and F. Cerrina
A scalable method for multiplex LED-controlled synthesis of DNA in capillaries
Nucleic Acids Res., September 11, 2006; 34(16): e110 - e110.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. B. Beres, E. W. Richter, M. J. Nagiec, P. Sumby, S. F. Porcella, F. R. DeLeo, and J. M. Musser
Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus
PNAS, May 2, 2006; 103(18): 7059 - 7064.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
A. E. Urban, J. O. Korbel, R. Selzer, T. Richmond, A. Hacker, G. V. Popescu, J. F. Cubells, R. Green, B. S. Emanuel, M. B. Gerstein, et al.
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays
PNAS, March 21, 2006; 103(12): 4534 - 4539.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Cattaruzza, A. Cricenti, A. Flamini, M. Girasole, G. Longo, T. Prosperi, G. Andreano, L. Cellai, and E. Chirivino
Controlled loading of oligodeoxyribonucleotide monolayers onto unoxidized crystalline silicon; fluorescence-based determination of the surface coverage and of the hybridization efficiency; parallel imaging of the process by Atomic Force Microscopy
Nucleic Acids Res., February 28, 2006; 34(4): e32 - e32.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
C.-w. Wu, J. Glasner, M. Collins, S. Naser, and A. M. Talaat
Whole-Genome Plasticity among Mycobacterium avium Subspecies: Insights from Comparative Genomic Hybridizations
J. Bacteriol., January 15, 2006; 188(2): 711 - 723.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
U. H. Manjunatha, H. Boshoff, C. S. Dowd, L. Zhang, T. J. Albert, J. E. Norton, L. Daniels, T. Dick, S. S. Pang, and C. E. Barry III
Identification of a nitroimidazo-oxazine-specific protein involved in PA-824 resistance in Mycobacterium tuberculosis
PNAS, January 10, 2006; 103(2): 431 - 436.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. L. Metzker
Emerging technologies in DNA sequencing
Genome Res., December 1, 2005; 15(12): 1767 - 1776.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
V. Stolc, M. P. Samanta, W. Tongprasit, and W. F. Marshall
Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes
PNAS, March 8, 2005; 102(10): 3703 - 3707.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
P. Bertone, V. Stolc, T. E. Royce, J. S. Rozowsky, A. E. Urban, X. Zhu, J. L. Rinn, W. Tongprasit, M. Samanta, S. Weissman, et al.
Global Identification of Human Transcribed Sequences with Genome Tiling Arrays
Science, December 24, 2004; 306(5705): 2242 - 2246.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. E. Richmond, M.-H. Li, M. J. Rodesch, M. Patel, A. M. Lowe, C. Kim, L. L. Chu, N. Venkataramaian, S. F. Flickinger, J. Kaysen, et al.
Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis
Nucleic Acids Res., September 24, 2004; 32(17): 5011 - 5018.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Baum, S. Bielau, N. Rittner, K. Schmid, K. Eggelbusch, M. Dahms, A. Schlauersbach, H. Tahedl, M. Beier, R. Guimil, et al.
Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling
Nucleic Acids Res., December 1, 2003; 31(23): e151 - e151.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.