Home LiteratureArticle Details
PMID: 3092188 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Quantitative analysis of the relationship between nucleotide sequence and functional activity.

Nucleic acids research ·Vol. 14 ·No. 16 ·1986-08-26 ·Pages 6661-79

Stormo GD, Schneider TD, Gold L

Abstract

Matrices can be used to evaluate sequences for functional activity. Multiple regression can solve for the matrix that gives the best fit between sequence evaluations and quantitative activities. This analysis shows that the best model for context effects on suppression by su2 involves primarily the two nucleotides 3' to the amber codon, and that their contributions are independent and additive. Context effects on 2AP mutagenesis also involve the two nucleotides 3' to the 2AP insertion, but their effects are not independent. In a construct for producing beta-galactosidase, the effects on translational yields of the tri-nucleotide 5' to the initiation codon are dependent on the entire triplet. Models based on these quantitative results are presented for each of the examples.

MeSH Terms
Base Sequence Codon DNA/genetics,metabolism Genes Mutation Peptide Chain Initiation, Translational Protein Biosynthesis Structure-Activity Relationship beta-Galactosidase/genetics
Chemicals
Codon DNA beta-Galactosidase
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Stormo G D
Schneider T D
Gold L
References (20)
20 references, click to expand
  1. Improved estimation of secondary structure in ribonucleic acids.
    Nat New Biol. 1973 Nov 14;246(150):40-1 PMID: 4519026
  2. Mutagenesis of the three bases preceding the start codon of the beta-galactosidase mRNA and its effect on translation in Escherichia coli.
    EMBO J. 1984 Mar;3(3):623-9 PMID: 6425057
  3. 2-Aminopurine.
    Mutat Res. 1980 Jan;75(1):1-47 PMID: 6987505
  4. Translational initiation in prokaryotes.
    Annu Rev Microbiol. 1981;35:365-403 PMID: 6170248
  5. Characterization of translational initiation sites in E. coli.
    Nucleic Acids Res. 1982 May 11;10(9):2971-96 PMID: 7048258
  6. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
    Nucleic Acids Res. 1982 May 11;10(9):2997-3011 PMID: 7048259
  7. A computer algorithm for testing potential prokaryotic terminators.
    Nucleic Acids Res. 1984 May 25;12(10):4411-27 PMID: 6374619
  8. On the molecular basis of transition mutations. Frequency of forming 2-aminopurine-cytosine base mispairs in the G X C----A X T mutational pathway by T4 DNA polymerase in vitro.
    J Biol Chem. 1984 Oct 10;259(19):11713-7 PMID: 6480580
  9. Mechanism and control of transcription initiation in prokaryotes.
    Annu Rev Biochem. 1985;54:171-204 PMID: 3896120
  10. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli.
    J Mol Biol. 1985 Nov 5;186(1):117-28 PMID: 3908689
  11. The context effect does not require a fourth base pair.
    Science. 1986 Jan 24;231(4736):393-5 PMID: 3510456
  12. A design for computer nucleic-acid-sequence storage, retrieval, and manipulation.
    Nucleic Acids Res. 1982 May 11;10(9):3013-24 PMID: 7099972
  13. Effects of surrounding sequence on the suppression of nonsense codons.
    J Mol Biol. 1983 Feb 15;164(1):59-71 PMID: 6188840
  14. Context effects: translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message.
    J Mol Biol. 1983 Feb 15;164(1):73-87 PMID: 6188841
  15. Search algorithm for pattern match analysis of nucleic acid sequences.
    Nucleic Acids Res. 1983 May 11;11(9):2943-57 PMID: 6344023
  16. Delila system tools.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):129-40 PMID: 6694897
  17. Computer methods to locate signals in nucleic acid sequences.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):505-19 PMID: 6364039
  18. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):789-800 PMID: 6364042
  19. Mutational analysis of a regulatory region in bacteriophage lambda that has overlapping signals for the initiation of transcription and translation.
    Proc Natl Acad Sci U S A. 1984 Jan;81(2):555-9 PMID: 6229793
  20. Molecular basis of base substitution hotspots in Escherichia coli.
    Nature. 1978 Aug 24;274(5673):775-80 PMID: 355893
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/14.16.6661
Published
1986-08-26
Pages
6661-79
Language
English
Region
England
NLM ID
0411011
PMCID
PMC311672
Subset
IM
Grants
NIGMS NIH HHS · GM28755 · United States
NCRR NIH HHS · RR01538 · United States
External Links
PubMed source DOI: 10.1093/nar/14.16.6661 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2