Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: Application to HIV genome

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Matveeva, Olga V ^a   Foley, Brian T ^b   Nemtsov, Vladimir A ^c   Gesteland, Raymond F ^a   Matsufuji, Senya ^d   Atkins, John F ^a,e   Ogurtsov, Aleksey Y ^f   Shabalina, Svetlana A ^f  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c MGGT   (Russian Federation)

^d JIKEI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^e UNIVERSITY COLLEGE CORK   (Ireland)

^f NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONSENSUS SEQUENCE; DNA OLIGONUCLEOTIDES; HYBRIDIZATION EFFICIENCY; INTERMOLECULAR INTERACTIONS; MULTIPLE SEQUENCE ALIGNMENTS; OLIGONUCLEOTIDE HYBRIDIZATION; SEQUENTIAL FILTERING; THERMODYNAMIC APPROACHES;

DNA; DNA SEQUENCES; GENES; MOLECULAR STRUCTURE; OPTIMIZATION; RNA; THERMODYNAMICS;

OLIGONUCLEOTIDES;

DNA; OLIGONUCLEOTIDE; RNA; GAG PROTEIN; VIRUS DNA; VIRUS RNA;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; GENE IDENTIFICATION; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMIC IN SITU HYBRIDIZATION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PROMOTER REGION; PROTEIN INTERACTION; PROTEIN TARGETING; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; THERMODYNAMICS; VIRUS GENOME; BIOLOGY; CONSENSUS SEQUENCE; GENETIC DATABASE; GENETICS; INTERNET; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; PROCEDURES;

HUMAN IMMUNODEFICIENCY VIRUS 1;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSENSUS SEQUENCE; DATABASES, GENETIC; DNA, VIRAL; GENE PRODUCTS, GAG; GENETIC VARIATION; GENOME, VIRAL; HIV-1; INTERNET; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; RNA, VIRAL; SEQUENCE ALIGNMENT; SOFTWARE; THERMODYNAMICS;

EID: 2942574534     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-44     Document Type: Article

References (22)

1. Walker GT, Fraiser MS, Schram JL, Little MC, Nadeau JG, Malinowski DP: Strand displacement amplification - an isothermal, in vitro DNA amplification technique. Nucleic Acids Res 1992, 20: 1691-1696.
2. Walker GT, Little MC, Nadeau JG, Shank DD: Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. Proc Natl Acad Sci USA 1992, 89: 392-396.
3. Kacian DL, Fultz TJ: Nucleic Acid Sequence Amplification Methods U.S. Patent No. 5.399.491; 1995.
4. Compton J: Nucleic acid sequence-based amplification. Nature 1991, 350: 91-92
5. Arnold LJ, Jr, Hammond PW, Wiese WA, Nelson NC: Assay formats involving acridinium-esterlabeled DNA probes. Clin Chem 1989, 35: 1588-1594.
6. Urdea MS, Wilber JC, Yeghiazarian T, Todd JA, Kern DG, Fong SJ, Besemer D, Hoo B, Sheridan PJ, Kokka R, Neuwald P, Pachl CA: Direct and quantitative detection of HIV-1 RNA in human plasma with a branched DNA signal amplification assay. Aids 1993, 7: Suppl 2, S11-14.
7. Urdea MS: Branched DNA signal amplification Biotechnology (N Y); 1994: 12: 926-928,.
8. DeLong EF, Wickham GS, Pace NR: Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 1989, 243: 1360-1363.
9. Amann RI, Ludwig W, Schleifer KH: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59: 143-169.
10. Chew CB, Zheng F, Byth K, Van Asten M, Workman C, Dwyer DE: Comparison of three commercial assays for the quantification of plasma HIV-1 RNA from individuals with low viral loads. Aids 1999, 13: 1977-1978.
11. Debyser Z, Van Wijngaerden E, Van Laethem K, Beuselinck K, Reynders M, De Clercq E, Desmyter J., Vandamme AM: Failure to quantify viral load with two of the three commercial methods in a pregnant woman harboring an HIV type 1 subtype G strain. AIDS Res Hum Retroviruses 1998, 14: 453-459.
12. Higgins DG, Sharp PM: CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 1988, 73: 237-244. [http://www.ebi.ac.uk/clustalw/]
13. Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF, Atkins JF: Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res 2003, 31: 4211-4217.
14. Matveeva OV, Mathews DH, Tsodikov AD, Shabalina SA, Gesteland RF, Atkins JF, Freier SM: Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucleic Acids Res 2003, 31: 4989-4994.
15. Lucas K, Busch M, Mossinger S, Thompson JA: An improved microcomputer program for finding gene- or gene family- specific oligonucleotides suitable as primers for polymerase chain reactions or as probes. Comput Appl Biosci 1991, 7: 525-529.
16. Dopazo J, Rodriguez A, Saiz JC, Sobrino F: Design of primers for PCR amplification of highly variable genomes. Comput Appl Biosci 1993, 9: 123-125.
17. Proutski V, Holmes EC: Primer Master: a new program for the design and analysis of PCR primers. Comput Appl Biosci 1996, 12: 253-255.
18. Kel A, Ptitsyn A, Babenko V, Meier-Ewert S, Lehrach H: A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily. Bioinformatics 1998, 14: 259-270.
19. Gibbs A, Armstrong J, Mackenzie AM, Weiller GF: The GPRIME package: computer programs for identifying the best regions of aligned genes to target in nucleic acid hybridisation-based diagnostic tests, and their use with plant viruses. J Virol Methods 1998, 74: 67-76.
20. Rouillard JM, Zuker M, Gulari E: OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 2003, 31: 3057-3062.
21. Gaschen B, Kuiken C, Korber B, Foley B: Retrieval and on-the-fly alignment of sequence fragments from the HIV database. Bioinformatics 2001, 17: 415-418. [http://hivweb.lanl.gov/content/hiv-db/CONSENSUS/M_GROUP/Consensus.html, http://hivweb.lanl.gov/content/hiv-db/ALIGN_CURRENT/ALIGN-INDEX.html]
22. Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH: Predicting oligonucleotide affinity to nucleic acid targets. RNA 1999, 5: 1458-1469. [http://128.151.176.70/RNAstructure.html