A software for designing oligonucleotides for PCR-based long DNA synthesis

Samuel Khor; Marcus Bode; Hongye Ye; Mo Huang Li; Jackie Y. Ying

doi:10.1109/ICBBE.2009.5162244

A software for designing oligonucleotides for PCR-based long DNA synthesis

Samuel Khor^*, Marcus Bode, Hongye Ye, Mo Huang Li, Jackie Y. Ying

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Herein we present a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). The program divides the long input DNA sequence based on the input number of oligonucleotides, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures. The software has been successfully used in the design and synthesis of green fluorescent protein fragment (GFPuv) (760 bp), human protein kinase B-2 (PKB2) (1446 bp) and the promoter of human calcium-binding protein A4 (S100A4) (752 bp).

Original language	English
Title of host publication	3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009
DOIs	https://doi.org/10.1109/ICBBE.2009.5162244
State	Published - 2009
Externally published	Yes

Publication series

Name	3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009

Keywords

Gene assembly
Gene synthesis
Software

ASJC Scopus subject areas

Biotechnology
Biomedical Engineering

Access to Document

10.1109/ICBBE.2009.5162244

Cite this

Khor, S., Bode, M., Ye, H., Li, M. H., & Ying, J. Y. (2009). A software for designing oligonucleotides for PCR-based long DNA synthesis. In 3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009 Article 5162244 (3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009). https://doi.org/10.1109/ICBBE.2009.5162244

@inproceedings{07151197f7c0420095745ce86d4fe352,

title = "A software for designing oligonucleotides for PCR-based long DNA synthesis",

abstract = "Herein we present a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). The program divides the long input DNA sequence based on the input number of oligonucleotides, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures. The software has been successfully used in the design and synthesis of green fluorescent protein fragment (GFPuv) (760 bp), human protein kinase B-2 (PKB2) (1446 bp) and the promoter of human calcium-binding protein A4 (S100A4) (752 bp).",

keywords = "Gene assembly, Gene synthesis, Software",

author = "Samuel Khor and Marcus Bode and Hongye Ye and Li, \{Mo Huang\} and Ying, \{Jackie Y.\}",

year = "2009",

doi = "10.1109/ICBBE.2009.5162244",

language = "English",

isbn = "9781424429028",

series = "3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009",

booktitle = "3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009",

}

A software for designing oligonucleotides for PCR-based long DNA synthesis. / Khor, Samuel; Bode, Marcus; Ye, Hongye et al.
3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009. 2009. 5162244 (3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - A software for designing oligonucleotides for PCR-based long DNA synthesis

AU - Khor, Samuel

AU - Bode, Marcus

AU - Ye, Hongye

AU - Li, Mo Huang

AU - Ying, Jackie Y.

PY - 2009

Y1 - 2009

N2 - Herein we present a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). The program divides the long input DNA sequence based on the input number of oligonucleotides, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures. The software has been successfully used in the design and synthesis of green fluorescent protein fragment (GFPuv) (760 bp), human protein kinase B-2 (PKB2) (1446 bp) and the promoter of human calcium-binding protein A4 (S100A4) (752 bp).

AB - Herein we present a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). The program divides the long input DNA sequence based on the input number of oligonucleotides, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures. The software has been successfully used in the design and synthesis of green fluorescent protein fragment (GFPuv) (760 bp), human protein kinase B-2 (PKB2) (1446 bp) and the promoter of human calcium-binding protein A4 (S100A4) (752 bp).

KW - Gene assembly

KW - Gene synthesis

KW - Software

UR - https://www.scopus.com/pages/publications/72749125626

U2 - 10.1109/ICBBE.2009.5162244

DO - 10.1109/ICBBE.2009.5162244

M3 - Conference contribution

AN - SCOPUS:72749125626

SN - 9781424429028

T3 - 3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009

BT - 3rd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2009

ER -

A software for designing oligonucleotides for PCR-based long DNA synthesis

Abstract

Publication series

Keywords

ASJC Scopus subject areas

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