Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

被引：116

作者：

Urakawa, H

El Fantroussi, S

Smidt, H

Smoot, JC

Tribou, EH

Kelly, JJ

Noble, PA

Stahl, DA

机构：

[1] Univ Washington, Dept Civil & Environm Engn, Seattle, WA 98195 USA

[2] Loyola Univ, Dept Biol, Chicago, IL 60626 USA

来源：

APPLIED AND ENVIRONMENTAL MICROBIOLOGY | 2003年 / 69卷 / 05期

关键词：

D O I：

10.1128/AEM.69.5.2848-2856.2003

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

引用

收藏

页码：2848 / 2856

页数：9

相关论文

共 31 条

[21] Microchip arrays put DNA on the spot [J].

Service, RF .

SCIENCE, 1998, 282 (5388) :396-+

[22] Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays [J].

Small, J ;

Call, DR ;

Brockman, FJ ;

Straub, TM ;

Chandler, DP .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2001, 67 (10) :4708-4716

[23] THERMODYNAMIC PARAMETERS TO PREDICT STABILITY OF RNA/DNA HYBRID DUPLEXES [J].

SUGIMOTO, N ;

NAKANO, S ;

KATOH, M ;

MATSUMURA, A ;

NAKAMUTA, H ;

OHMICHI, T ;

YONEYAMA, M ;

SASAKI, M .

BIOCHEMISTRY, 1995, 34 (35) :11211-11216

[24] Regioselective immobilization of short oligonucleotides to acrylic copolymer gels [J].

Timofeev, EN ;

Kochetkova, SV ;

Mirzabekov, AD ;

Florentiev, VL .

NUCLEIC ACIDS RESEARCH, 1996, 24 (16) :3142-3148

[25] Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses [J].

Urakawa, H ;

Noble, PA ;

El Fantroussi, S ;

Kelly, JJ ;

Stahl, DA .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2002, 68 (01) :235-244

[26] Fabrication of microarray of gel-immobilized compounds on a chip by copolymerization [J].

Vasiliskov, AV ;

Timofeev, EN ;

Surzhikov, SA ;

Drobyshev, AL ;

Shick, VV ;

Mirzabekov, AD .

BIOTECHNIQUES, 1999, 27 (03) :592-+

[27] IN-SITU IDENTIFICATION OF AMMONIA-OXIDIZING BACTERIA [J].

WAGNER, M ;

RATH, G ;

AMANN, R ;

KOOPS, HP ;

SCHLEIFER, KH .

SYSTEMATIC AND APPLIED MICROBIOLOGY, 1995, 18 (02) :251-264

[28] High-density microarray of small-subunit ribosomal DNA probes [J].

Wilson, KH ;

Wilson, WJ ;

Radosevich, JL ;

DeSantis, TZ ;

Viswanathan, VS ;

Kuczmarski, TA ;

Andersen, GL .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2002, 68 (05) :2535-2541

[29] Development and evaluation of functional gene arrays for detection of selected genes in the environment [J].

Wu, LY ;

Thompson, DK ;

Li, GS ;

Hurt, RA ;

Tiedje, JM ;

Zhou, JZ .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2001, 67 (12) :5780-5790

[30] DNA analysis and diagnostics on oligonucleotide microchips [J].

Yershov, G ;

Barsky, V ;

Belgovskiy, A ;

Kirillov, E ;

Kreindlin, E ;

Ivanov, I ;

Parinov, S ;

Guschin, D ;

Drobishev, A ;

Dubiley, S ;

Mirzabekov, A .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (10) :4913-4918

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