Literature DB >> 8233815

A study of oligonucleotide reassociation using large arrays of oligonucleotides synthesised on a glass support.

U Maskos1, E M Southern.   

Abstract

An extensive analysis of oligonucleotide interactions was carried out by hybridising a synthetic pool of 256 10mers, A(C,T)8A, representing all oligopyrimidine octamer sequences to an array of four copies of all 256 different octapurine sequences. The resulting 256 duplexes were quantified by phosphorimaging and analysed to determine the dependence of duplex formation on base composition, sequence, and salt concentration. The results show that the base composition dependence of duplex formation can be reduced by high concentrations of tetramethylammonium chloride. This chaotropic solvent also increases duplex yield by up to fifty-fold.

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Year:  1993        PMID： 8233815      PMCID： PMC331488          DOI： 10.1093/nar/21.20.4663

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  19 in total

1.  Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models.

Authors:  E M Southern; U Maskos; J K Elder
Journal:  Genomics       Date:  1992-08       Impact factor: 5.736

2.  DNA melting temperatures and renaturation rates in concentrated alkylammonium salt solutions.

Authors:  J M Orosz; J G Wetmur
Journal:  Biopolymers       Date:  1977-06       Impact factor: 2.505

3.  A new method for sequencing DNA.

Authors:  A M Maxam; W Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  1977-02       Impact factor: 11.205

4.  Base composition-independent hybridization in tetramethylammonium chloride: a method for oligonucleotide screening of highly complex gene libraries.

Authors:  W I Wood; J Gitschier; L A Lasky; R M Lawn
Journal:  Proc Natl Acad Sci U S A       Date:  1985-03       Impact factor: 11.205

5.  Preparative two-dimensional polyacrylamide gel electrophoresis of 32 P-labeled RNA.

Authors:  R de Wachter; W Fiers
Journal:  Anal Biochem       Date:  1972-09       Impact factor: 3.365

6.  The binding of small cations to deoxyribonucleic acid. Nucleotide specificity.

Authors:  J T Shapiro; B S Stannard; G Felsenfeld
Journal:  Biochemistry       Date:  1969-08       Impact factor: 3.162

7.  Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA.

Authors:  W B Melchior; P H Von Hippel
Journal:  Proc Natl Acad Sci U S A       Date:  1973-02       Impact factor: 11.205

8.  Proton NMR study and conformational analysis of d(CGT), d(TCG) and d(CGTCG) in aqueous solution. The effect of a dangling thymidine and of a thymidine mismatch on DNA mini-duplexes.

Authors:  J R Mellema; R van der Woerd; G A van der Marel; J H van Boom; C Altona
Journal:  Nucleic Acids Res       Date:  1984-06-25       Impact factor: 16.971

9.  DNA sequencing with chain-terminating inhibitors.

Authors:  F Sanger; S Nicklen; A R Coulson
Journal:  Proc Natl Acad Sci U S A       Date:  1977-12       Impact factor: 11.205

10.  DNA chain length markers and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels.

Authors:  R Frank; H Köster
Journal:  Nucleic Acids Res       Date:  1979       Impact factor: 16.971
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  19 in total

1.  Modification of DNA duplexes to smooth their thermal stability independently of their base content for DNA sequencing by hybridization.

Authors:  H K Nguyen; P Auffray; U Asseline; D Dupret; N T Thuong
Journal:  Nucleic Acids Res       Date:  1997-08-01       Impact factor: 16.971

2.  High-throughput detection of pathogenic yeasts of the genus trichosporon.

Authors:  Mara R Diaz; Jack W Fell
Journal:  J Clin Microbiol       Date:  2004-08       Impact factor: 5.948

3.  Effects of target length on the hybridization efficiency and specificity of rRNA-based oligonucleotide microarrays.

Authors:  Wen-Tso Liu; Huiling Guo; Jer-Horng Wu
Journal:  Appl Environ Microbiol       Date:  2006-10-27       Impact factor: 4.792

Review 4.  Probing lymphocyte biology by genomic-scale gene expression analysis.

Authors:  A Alizadeh; M Eisen; D Botstein; P O Brown; L M Staudt
Journal:  J Clin Immunol       Date:  1998-11       Impact factor: 8.317

5.  Oligomeric structure of glycoproteins in herpes simplex virus type 1.

Authors:  C G Handler; R J Eisenberg; G H Cohen
Journal:  J Virol       Date:  1996-09       Impact factor: 5.103

6.  Hamming chromatography.

Authors:  A Schwienhorst; A Schober; R Günther; P F Stadler
Journal:  Mol Divers       Date:  1996-05       Impact factor: 2.943

7.  Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays.

Authors:  M S Shchepinov; S C Case-Green; E M Southern
Journal:  Nucleic Acids Res       Date:  1997-03-15       Impact factor: 16.971

8.  Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes.

Authors:  Jörg Peplies; Frank Oliver Glöckner; Rudolf Amann
Journal:  Appl Environ Microbiol       Date:  2003-03       Impact factor: 4.792

9.  The biophysics of DNA hybridization with immobilized oligonucleotide probes.

Authors:  V Chan; D J Graves; S E McKenzie
Journal:  Biophys J       Date:  1995-12       Impact factor: 4.033

10.  Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides.

Authors:  D I Stimpson; J V Hoijer; W T Hsieh; C Jou; J Gordon; T Theriault; R Gamble; J D Baldeschwieler
Journal:  Proc Natl Acad Sci U S A       Date:  1995-07-03       Impact factor: 11.205
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