Specific and nonspecific hybridization of oligonucleotide probes on microarrays

被引:53
作者
Binder, H [1 ]
Preibisch, S [1 ]
机构
[1] Univ Leipzig, Interdisciplinary Ctr Bioinformat, D-7010 Leipzig, Germany
关键词
D O I
10.1529/biophysj.104.055343
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
Gene expression analysis by means of microarrays is based on the sequence-specific binding of RNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving sequences other than the intended target is problematic because it adds a chemical background to the signal, which is not related to the expression degree of the target gene. The article presents a molecular signature of specific and nonspecific hybridization with potential consequences for gene expression analysis. We analyzed the signal intensities of perfect match (PM) and mismatch (MM) probes of GeneChip microarrays to specify the effect of specific and nonspecific hybridization. We found that these events give rise to different relations between the PM and MM intensities as function of the middle base of the PM, namely a triplet-like (C > G approximate to T > A > 0) and a duplet-like (C approximate to T > 0 > G approximate to A) pattern of the PM-MM log-intensity difference upon binding of specific and nonspecific RNA fragments, respectively. The systematic behavior of the intensity difference can be rationalized on the level of basepairings of DNA/RNA oligonucleotide duplexes in the middle of the probe sequence. Nonspecific binding is characterized by the reversal of the central Watson-Crick (WC) pairing for each PM/MM probe pair, whereas specific binding refers to the combination of a WC and a self-complementary (SC) pairing in PM and MM probes, respectively. The Gibbs free energy contribution of WC pairs to duplex stability is asymmetric for purines and pyrimidines of the PM and decreases according to C > G approximate to T > A. SC pairings on the average only weakly contribute to duplex stability. The intensity of complementary MM introduces a systematic source of variation which decreases the precision of expression measures based on the MM intensities.
引用
收藏
页码:337 / 352
页数:16
相关论文
共 37 条
[11]   Prediction of hybridization and melting for double-stranded nucleic acids [J].
Dimitrov, RA ;
Zuker, M .
BIOPHYSICAL JOURNAL, 2004, 87 (01) :215-226
[12]   Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios [J].
Dorris, DR ;
Nguyen, A ;
Gieser, L ;
Lockner, R ;
Lublinsky, A ;
Patterson, M ;
Touma, E ;
Sendera, TJ ;
Elghanian, R ;
Mazumder, A .
BMC BIOTECHNOLOGY, 2003, 3 (1)
[13]   Sensitivity, specificity, and the hybridization isotherms of DNA chips [J].
Halperin, A ;
Buhot, A ;
Zhulina, EB .
BIOPHYSICAL JOURNAL, 2004, 86 (02) :718-730
[14]   Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays [J].
Hekstra, D ;
Taussig, AR ;
Magnasco, M ;
Naef, F .
NUCLEIC ACIDS RESEARCH, 2003, 31 (07) :1962-1968
[15]   Modeling of DNA microarray data by using physical properties of hybridization [J].
Held, GA ;
Grinstein, G ;
Tu, Y .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (13) :7575-7580
[16]   Summaries of affymetrix GeneChip probe level data [J].
Irizarry, RA ;
Bolstad, BM ;
Collin, F ;
Cope, LM ;
Hobbs, B ;
Speed, TP .
NUCLEIC ACIDS RESEARCH, 2003, 31 (04) :e15
[17]   Effect of oligonucleotide truncation on sing le-nucleotide distinction by solid-phase hybridization [J].
Jobs, M ;
Fredriksson, S ;
Brookes, AJ ;
Landegren, U .
ANALYTICAL CHEMISTRY, 2002, 74 (01) :199-202
[18]   Thermodynamics of single mismatches in RNA duplexes [J].
Kierzek, R ;
Burkard, ME ;
Turner, DH .
BIOCHEMISTRY, 1999, 38 (43) :14214-14223
[19]   Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection [J].
Li, C ;
Wong, WH .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (01) :31-36
[20]   High density synthetic oligonucleotide arrays [J].
Lipshutz, RJ ;
Fodor, SPA ;
Gingeras, TR ;
Lockhart, DJ .
NATURE GENETICS, 1999, 21 (Suppl 1) :20-24