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Gene synthesis from photolithographi...

Kim, Changhan.

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Gene synthesis from photolithographic DNA microarrays.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Gene synthesis from photolithographic DNA microarrays./
Author:	Kim, Changhan.
Description:	218 p.
Notes:	Adviser: Franco Cerrina.
Contained By:	Dissertation Abstracts International68-04B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3261401

Gene synthesis from photolithographic DNA microarrays.
Kim, Changhan.

Gene synthesis from photolithographic DNA microarrays. - 218 p.

Adviser: Franco Cerrina.

Thesis (Ph.D.)--The University of Wisconsin - Madison, 2007.

The capability of synthesizing hundreds of thousand different oligonucleotides on a DNA microarray led to the idea of the gene assembly from a DNA microarray. Its proof of concept was demonstrated by our research group for the first time in 2004. In the DNA assembly from chip-eluted oligonucleotides, the most challenging part is to obtain pure oligonucleotides; sequence errors are inevitably formed during synthesis regardless of synthesis platforms. Hence, intensive filtering of erroneous oligonucleotides has been researched prior to an actual DNA assembly by many groups---post-synthesis error correction.Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Gene synthesis from photolithographic DNA microarrays.
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035 $a (UMI)AAI3261401
035 $a AAI3261401
040 $a UMI $c UMI
100 1 $a Kim, Changhan. $3 1271051
245 1 0 $a Gene synthesis from photolithographic DNA microarrays.
300 $a 218 p.
500 $a Adviser: Franco Cerrina.
500 $a Source: Dissertation Abstracts International, Volume: 68-04, Section: B, page: 2546.
502 $a Thesis (Ph.D.)--The University of Wisconsin - Madison, 2007.
520 $a The capability of synthesizing hundreds of thousand different oligonucleotides on a DNA microarray led to the idea of the gene assembly from a DNA microarray. Its proof of concept was demonstrated by our research group for the first time in 2004. In the DNA assembly from chip-eluted oligonucleotides, the most challenging part is to obtain pure oligonucleotides; sequence errors are inevitably formed during synthesis regardless of synthesis platforms. Hence, intensive filtering of erroneous oligonucleotides has been researched prior to an actual DNA assembly by many groups---post-synthesis error correction.
520 $a In this thesis work, I emphasize error prevention/reduction during oligonucleotide synthesis rather than resorting to post-synthesis error purification. For "in-situ" synthesis improvement, the complete knowledge of the synthesis chemistry and optical system is required. From this, prediction and verification of synthesis improvement can be made through modeling and experiments respectively.
520 $a We developed the second generation of the MAS (Maskless Array Synthesizer) to implement an in-situ light-directed parallel oligonucleotides synthesis for synthesizing oligonucleotides for DNA assembly. To understand how sequence errors are formed and distributed on the DNA microarrays fabricated by the MAS, several DNA synthesis models, including a comprehensive stochastic synthesis model using Monte-Carlo simulation, were developed and their validity was verified through experiments. An error prevention system ("image locking") and an error prevention method ("inverse capping") were developed to improve the quality of the synthetic oligonucleotides. The models were also successfully used in tuning the synthesis system and synthesis process by extracting synthesis parameters through simulation and experiments.
590 $a School code: 0262.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Biology, Molecular. $3 1017719
650 4 $a Engineering, Electronics and Electrical. $3 626636
690 $a 0307
690 $a 0544
690 $a 0715
710 2 $a The University of Wisconsin - Madison. $3 626640
773 0 $t Dissertation Abstracts International $g 68-04B.
790 $a 0262
790 1 0 $a Cerrina, Franco, $e advisor
791 $a Ph.D.
792 $a 2007
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3261401