Oligonucleotide microarray for human immunodeficiency virus detection

Abstract

Abstract: Objective To develop an oligonucleotide microarray for fast detection of human immunodeficiency virus (HIV).Methods With complete genome sequence of HIV-1 subtype B (U26942) as the target sequence and bioinformatics software such as DNAClub, Oligo6.0, BLAST, Alignment, oligonucleotide probes of high specificity with identical length and similar melting temperature (T_m) were designed and synthesized. Oligonucleotide microarray was prepared using Cartesian Microarrayer. Using the plasmids of HIV-1 subtype B(U26942), C(U46016), F(AF075703), G(AF061640) and restriction display technique, Cy3-labeled HIV DNA fragments were amplified and the hybridization results were scanned and analyzed with Array-Pro.Results and Conclusion Twenty-two optimized oligonucleotide microarray probes were obtained and used to prepare the oligonucleotide microarray for further screening studies. The microarray prepared significantly enhanced the sensitivity, reliability and speed of DNA assay, and possesses the potential for application in clinical setting.

CLC Number:

WEN Ying¹, MA Wen-li¹, LI Ling¹, WU Qing-hua¹, XU Qiu-lin¹, ZHANG Hai-yan¹, ZHENG Wen-ling². Oligonucleotide microarray for human immunodeficiency virus detection[J]. Journal of Southern Medical University, 2005, 25(03): 293-297.

References

[1] Portsmouth S,Stebbing J,Keyi X,et al. HIV and AIDS in the People’s Republic of China:a collaborative review [J]. Int J STD AIDS,2003,14(11):757-61.
[2] http://phorum.nst.pku.edu.cn/showthread.php?threadid=723
[3] Salminen MO,Koch C,Sanders-Buell E,et al. Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction [J]. Virology,1995,213(1):80-6.
[4] Li L,Ma WL,Zhu J,et al. A modified restriction display PCR method in sample-labeling of DNA microarray [J]. J Virol Methods,2003,114(1):71-5.
[5] 李凌,马文丽,宋艳斌,等.HIV-1基因限制性显示片段的克隆与序列分析[J].第一军医大学学报,2001,21(11):815-81.Li L,Ma WL,Song YB,et al. Cloning and sequence analysis of HIV-1 gene fragments isolated by restriction digest polymerase chain reaction method [J]. J First Mil Med Univ/Di Yi Jun Yi Da Xue Xue Bao,2001,21(11):815-81.
[6] http://www.hicomb.org/papers/HICOMB2003 -05.pdf
[7] Fugen Li,Gary D. Selection ofoptimal DNA oligos for gene expression arrays[J]. Bioinformatics,2001,17(11):1067-76.
[8] 邢玉兰.艾滋病病原学诊断进展[J].中华检验医学杂志(Chin J Lab Med),2001,24(3):188-9.
[9] 石嵘,马文丽,吴清华,等.用于SARS冠状病毒检测的60mer寡核苷酸基因芯片的设计及应用[J].科学通报,2003,48(12):1237-41.Shi R,Ma WL,Wu QH,et al. Design and application of 60mer oligouncleotide microarray in SARS coronavirus detection [J]. Chin Sci Bull,2003,48(12):1237-41.
[10] 王艳,马文丽,毛向明,等.痘苗病毒寡核苷酸检测芯片的设计及研制[J].第一军医大学学报,2004,24(2):180-3.Wang Y,Ma WL,Mao XM,et al. Design and preparation of oligonucleotide microarray for vaccinia virus detection [J]. J First Mil Med Univ/Di Yi Jun Yi Da Xue Xue Bao,2004,24(2):180-3.
[11] Angela Relogio,Christian Schwager,Alexandra Richter,et al.Optimization of oligonucleotide-based DNA microarrays [J].Nucleic Acids Res,2002,30(11):e51.

Related Articles 15

[1]	ZHANG Lei1,2,CHEN Jian-ping1,2,ZHANG Li1,2,WANG Tao1,LIU Ming-jie1,TIAN Yu1 Department of Parasiotology1,Key Laboratory of Chronobiology of Ministry of Health2,West China Medical Center,Sichuan University,Chengdu 610041,China. Construction of a prokaryotic expression vector carrying mompS-linker-flaA fusion gene and its expression in E.coli [J]. Journal of Southern Medical University, 2006, 26(12): 1701-1705.
[2]	WANG Quan-shi1,WANG Xin-lu2,LI Hua3,WANG Qiao-yu1,WANG Quan-ying4,YANG Guang-xiao4 1PET Center,Nanfang Hospital,Southern Medical University,Guangzhou 510515,China;2PET Center of Department of Nuclear Medicine,Guangzhou General Hospital of Guangzhou Command,Guangzhou 510010,China;3Third Affiliated Hospital of Sun Yat-sen University,Guangzhou 510630,China;4Xi’an Huaguang Bioengineering Company,Xi’an 710025,China. Construction of a retroviral vector for RNA interference targeting human telomerase reverse transcriptase [J]. Journal of Southern Medical University, 2006, 26(12): 1715-1719.
[3]	LI De-liang,MA Wen-li,SHI Yong-xia,LI Ling,ZHANG Bao,ZHENG Wen-ling Institute of Genetic Engineering,Southern Medical University,Guangzhou 510515,China. Construction of a eukaryotic expression plasmid containing gp120 gene of HIV-1 subtype B and its expression in HepG2 cells [J]. Journal of Southern Medical University, 2006, 26(12): 1724-1727.
[4]	YUAN Ai-qin,HE Yuan-li,YANG Fang,LIU Mu-biao Department of Obstetrics and Gynecology,Zhujiang Hospital,Southern Medical University,Guangzhou 510282,China. Construction of a recombinant adenoviral vector expressing human endostatin [J]. Journal of Southern Medical University, 2006, 26(12): 1769-1771.
[5]	JIANG Hong-chao1,2,SUN Qiang-ming1,ZHAO Dan2,SUN Mao-sheng1,LU Lin2,LI Hong-jun1 1Department of Molecular Biology,Institute of Medical Biology,Chinese Academy of Medical Sciences and Peking Union Medical College,Kunming 650118,China;2Graduate School of Kunming Medical College,Kunming 650031,China. RNA interference-mediated inhibition of survivin expression in Hela cell line by siRNA expression vector targeting survivin gene [J]. Journal of Southern Medical University, 2006, 26(12): 1806-1811.
[6]	SHAO Zi-yun,LIU Zhi-feng,PENG Yi,XU Jia,DENG Peng,JIANG YongKey Laboratory of Functional Proteomics of Guangdong Province,Southern Medical University,Guangzhou 510515,Chin. Construction of a recombinant adenovirus vector for interferon-γ-inducible protein 10 and the adenovirus preparation [J]. Journal of Southern Medical University, 2006, 26(11): 1552-1555.
[7]	MA Shu-dong1,LUO Rong-cheng1,DING Zheng-hua2,YUAN Chang-qing2,DING Xue-mei1 Department of Oncology,Nanfang Hospital1,Department of Radiation Medicine,Institute of Tropical Medicine2,Southern Medical University,Guangzhou 501515,Chin. Construction and identification of recombinant adenoviruses containing the gene fragments encoding Her2/neu extracellular and transmembrane domains [J]. Journal of Southern Medical University, 2006, 26(11): 1641-.
[8]	LI Hai-yu, GUO Ai-hua, LIU Zhi-feng, LIU Yu, LIU Jing-hua, DENG Peng, LI Zhi-jie, LIU Ya-wei, JIANG Yong Department of Pathophysiology and Key Laboratory of Functional Proteomics of Guangdong Province, Southern Medical University, Guangzhou 510515, China. Construction and functional study of a cell penetrating peptide-based expression vector for targeted delivery of proteins into the cell nuclei [J]. Journal of Southern Medical University, 2006, 26(10): 1394-.
[9]	YANG Pei1, WANG Kun-zheng1, SHI Zhi-bin1, DANG Xiao-qian1, YU Peng-bo2, WANG Chun-sheng1, GONG Fu-liang3 1Department of Orthopedics, Second Affiliated Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an 710004, China; 2Institute of Virus Research, Center for Disease Control and Prevention of Shaanxi Province, Xi’an 710054, China; 3Department of Orthopedics, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China. Prokaryotic expression, purification and activity assay of recombinant vascular endothelial growth factor [J]. Journal of Southern Medical University, 2006, 26(09): 1263-1268.
[10]	XING Rui, YANG Xiao-qiang, CHEN Xue-qing, ZHANG Zhen-shu Institute for Digestive Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China. Construction of Lactococcus lactis expression vector of recombinant human trefoil factor family 2 [J]. Journal of Southern Medical University, 2006, 26(09): 1280-1283.
[11]	REN Shu-ting1, YU Lin-hua1, XU Chang-fu1, GAO Guang-dao2 Department of Pathology1, Department of Physiology and Pathophysiology2, Medical College of Xi’an Jiaotong University, Xi’an 710061, China. Construction and identification of tetracycline-inducible rat Smad7 eukaryotic expression vector [J]. Journal of Southern Medical University, 2006, 26(09): 1313-1315.
[12]	DONG Xiao1,2, WANG Jia-ning1, HUANG Yong-zhang1, GUO Ling-yun1 1Institute of Clinical Medicine, People’s Hospital of Yunyang Medical College, Shiyan 442000, China; 2School of Medicine, Wuhan University, Wuhan 430060, China. Expression and purification of PEP-1-EGFP fusion protein and its transduction into human umbilical vein endothelial cells [J]. Journal of Southern Medical University, 2006, 26(08): 1114-1117.
[13]	LIU Ming-Jie1, CHEN Jian-ping1, WANG Tao1, LIAO Tao2, CHEN Xian1, LU Dian-xiang3, TIAN Yu1 1Department of Parasitology, West China Medical Center, Sichuan University, Chengdu 610041, China; 2Department of Diagnostics, North Sichuan Medical College, Luzhou 637000, China; 3Biomaterial Engineering Research Center, Sichuan University, Chengdu 610064, China. Legionella pneumophila lvgA and Hsp60 gene splicing and the fusion gene expression in E. coli [J]. Journal of Southern Medical University, 2006, 26(07): 904-909.
[14]	LI Yan, BAO Lang, ZHANG Hui-dong, LI Ya-sha, ZHU Hai-long Laboratory of Infection and Immunity, College of Preclinical and Forensic Medicine, West China Medical Center of Sichuan University, Chengdu 610041, China. Construction of recombinant Mycobacterium smegmatis expressing ESAT-6 and its effects on macrophages [J]. Journal of Southern Medical University, 2006, 26(07): 923-926.
[15]	ZOU Hong-Yun1, MA Li1, YAO Xin-sheng1, WEN Qian1, LUO Wei1, WANG Xiao-Ning2 1Institute of Molecular Immunology, School of Biotechnology, Southern Medical University, Guangzhou 510515, China; 2School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510641, China. Effects of T cell receptor gene rearrangement on BV CDR3 in Jurkat cells [J]. Journal of Southern Medical University, 2006, 26(07): 939-943.