|本期目录/Table of Contents|

[1]马琴琴,严国权,郭江峰,等. 影响RNA芯片探针杂交效率的因素分析[J].浙江理工大学学报,2012,29(04):599-603.
 MA Qin qin,YAN Guo quan,GUO Jiang feng,et al. Factors Analysis of Oligodeoxyribonucleotide Probes for RNA Microarray[J].Journal of Zhejiang Sci-Tech University,2012,29(04):599-603.
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 影响RNA芯片探针杂交效率的因素分析()
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浙江理工大学学报[ISSN:1673-3851/CN:33-1338/TS]

卷:
第29卷
期数:
2012年04期
页码:
599-603
栏目:
(自科)生物与生命科学
出版日期:
2012-08-28

文章信息/Info

Title:
 Factors Analysis of Oligodeoxyribonucleotide Probes for RNA Microarray
文章编号:
16733851 (2012) 04059905
作者:
 马琴琴 严国权 郭江峰 丁先锋
 浙江理工大学生命科学学院生物工程研究所, 杭州 310018
Author(s):
 MA Qinqin YAN Guoquan GUO Jiangfeng DING Xianfeng
 Institute of Bioengineering, School of Life Sciences, Zhejiang SciTech University,Hangzhou 310018, China
关键词:
 覆瓦式探针 RNA芯片 二级结构 探针/靶序列杂交双链
分类号:
Q789
文献标志码:
A
摘要:
     RNA芯片作为研究ncRNA的主要技术之一,已受到广泛关注。然而因RNA芯片中靶序列的单链特征,使得RNA芯片的探针设计比DNA复杂。本研究对加强型绿色荧光蛋白(EGFP)RNA序列进行覆瓦式探针设计,〖JP2〗制作了RNA原位合成芯片,研究探针/靶序列杂交双链ΔG和Tm、靶序列二级结构以及探针的末端碱基对RNA芯片杂交信号强度的影响。结果表明,探针/靶序列杂交双链ΔG和Tm相同的探针间的杂交信号存在较大差异,探针/靶序列杂交双链ΔG和Tm与RNA芯片杂交信号之间未发现明显的规律性;靶序列二级结构的探针PTsc参数与芯片杂交信号强度间呈较好的线性关系;探针5’末端碱基组成对芯片杂交信号强度也有影响,5’末端碱基为G/C的探针杂交信号总体上高于其邻近的5’末端碱基为A/T的探针的杂交信号,为RNA芯片的探针筛选提供一定的理论基础

参考文献/References:

 [1] He D, Zaitlen N, Pasaniuc B, et al. Genotyping common and rare variation using overlapping pool sequencing[J]. BMC Bioinformatics, 2011, 12(S6): S2.
[2] Kong W, Mou X, Hu X. Exploring matrix factorization techniques for significant genes identification of alzheimers disease microarray gene expression data[J]. BMC Bioinformatics, 2011, 12(S5): S7.
[3] Lazaridis E N, Sinibaldi D, Bloom G, et al. A simple method to improve probe set estimates from oligonucleotide arrays[J]. Math Biosci, 2002, 176(1): 5358.
[4] Saidi S A, Holland C M, Kreil D P, et al. Independent component analysis of microarray data in the study of endometrial cancer[J]. Oncogene, 2004, 23(39): 66776683.
[5] Wei H, Kuan P F, Tian S, et al. A study of the relationships between oligonucleotide properties and hybridization signal intensities from nimblegen microarray datasets[J]. Nucleic Acids Res, 2008, 36(9): 29262938.
[6] Chou H H, Hsia A P, Mooney D L, et al. Picky: oligo microarray design for large genomes[J]. Bioinformatics, 2004, 20(17): 28932902.
[7] Rouillard J M, Zuker M, Gulari E. Oligoarray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach[J]. Nucleic Acids Res, 2003, 31(12): 30573062.
[8] Luebke K J, Balog R P, Garner H R. Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts[J]. Nucleic Acids Res, 2003, 31(2): 750758.
[9] Reymond N, Charles H, Duret L, et al. Roso: optimizing oligonucleotide probes for microarrays[J]. Bioinformatics, 2004, 20(2): 271273.
[10] Wang X, Seed B. Selection of oligonucleotide probes for protein coding sequences[J]. Bioinformatics, 2003, 19(7): 796802.
[11] Ratushna V G, Weller J W, Gibas C J. Secondary structure in the target as a confounding factor in synthetic oligomer microarray design[J]. BMC Genomics, 2005, 6: 31.
[12] Nielsen H B, Wernersson R, Knudsen S. Design of oligonucleotides for microarrays and perspectives for design of multitranscriptome arrays[J]. Nucleic Acids Res, 2003, 31(13): 34913496.
[13] DalmaWeiszhausz D D, Warrington J, Tanimoto E Y, et al. The affymetrix genechip platform: an overview[J]. Methods Enzymol, 2006, 410: 328.
[14] Held G A, Grinstein G, Tu Y. Modeling of DNA microarray data by using physical properties of hybridization[J]. Proc Natl Acad Sci USA, 2003, 100(13): 75757580.
[15] Matera A G, Terns R M, Terns M P. Noncoding RNAs: lessons from the small nuclear and small nucleolar RNAs[J]. Nat Rev Mol Cell Biol, 2007, 8(3): 209220.
[16] Yin J Q, Zhao R C. Identifying expression of new small RNAs by microarrays[J]. Methods, 2007, 43(2): 123130.
[17] Zuker M. Mfold web server for nucleic acid folding and hybridization prediction[J]. Nucleic Acids Res, 2003, 31(13): 34063415.
[18] Mathews D H, Sabina J, Zuker M, et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure[J]. J Mol Biol, 1999, 288(5): 911940.
[19] Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information[J]. Nucleic Acids Res, 1981, 9(1): 133148.
[20] Mathews D H. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization[J]. RNA, 2004, 10(8): 11781190.

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备注/Memo

备注/Memo:
 收稿日期: 2011-11-22
基金项目: 国家高技术研究发展计划项目(863计划,2007AA02Z165);广东省教育部产学研结合项目(2011B090400478);浙江省自然科学基金项目(Y2100681);杭州市科技发展计划项目(20110733Q04,20110733Q21)
作者简介: 马琴琴(1986-),女,湖北荆州人,硕士研究生,从事生物化学与分子生物学研究。
通讯作者: 丁先锋,Email:xfding@zstu.edu.cn
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