New triphosphate conjugates bearing reporter groups: Labeling of DNA fragments for microarray analysis

Bioconjugate Chemistry

Volumn 18, Issue 3, 2007, Pages 886-893

  Alexandrova, Ludmila A ^a   Jasko, Maxim V ^a   Belobritskaya, Elena E ^a   Chudinov, Alexander V ^a   Mityaeva, Olga N ^a   Nasedkina, Tatyana V ^a   Zasedatelev, Alexander S ^a   Kukhanova, Marina K ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; POLYMERASE CHAIN REACTION;

CALF THYMUS; DNA FRAGMENT; LABELINGS; LIGAND GROUPS; MICROARRAY ANALYSIS; MONOESTERS; SIMPLE++; SYNTHESISED; TARGET PREPARATION; TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE;

FLUORESCENCE;

BIOTIN; DNA FRAGMENT; DNA NUCLEOTIDYLEXOTRANSFERASE; ESTER DERIVATIVE; FLUORESCENT DYE; LIGAND; PHOSPHATE; PHOSPHORIC ACID DERIVATIVE;

3' UNTRANSLATED REGION; ARTICLE; CONJUGATE; DNA MICROARRAY; MICROARRAY ANALYSIS; POLYMERASE CHAIN REACTION; SYNTHESIS; TECHNIQUE;

EID: 34347352235     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc060213z     Document Type: Article

References (23)

1. Hermanson, G. T. (1996) Bioconjugate Techniques, pp 640-671, Academic Press, New York.
2. Kricka, L. J. (1992) Nonisotopic DNA probe techniques, Academic Press, San Diego.
3. Ranasinghe, R. T., and Brown, T. (2005) Fluorescent based strategies for genetic analysis. Chem. Commun. 5487-5502.
4. Duthie, R. S., Kalve, I. M., Samols, S. B., Hamilton, S., Livshin, I., Khot, M., Nampalli, S., Kumar, S., and Fuller, C. W. (2002) Novel Cyanine Dye-labeled Dideoxynucleoside Triphosphates for DNA Sequencing. Bioconjugate Chem. 13, 699-706.
5. Godovikova, T. S., Kolpashchikov, D. M., Orlova, T. N., Richter, V. A., Ivanova, T. M., Grochovsky, S. L., Nasedkina, T. V., Victorova, L. S., and Poletaev, A. I. (1999) 5-[3-(E)-4-Azido-2,3,5,6-tetrafluorobenzamido) propenyl-1]-2′-deoxyuridine-5′-triphosphate substitutes for thymidine-5′-triphosphate in the polymerase chain reaction. Bioconjugate Chem. 10, 529-537.
6. Giller, G., Tasara, T., Angerer, B., Mulleger, K., Amacker, M., and Winter, H. (2003) Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. I. Chemical synthesis of various reporter group-labeled 2′-deoxyribonucleoside-5′-triphosphates. Nucleic Acids Res. 31, 2630-2635.
7. Tasara, T., Angerer, B., Damond, M., Winter, H., Dorhofer, S., Hubscher, U., and Amacker, M. (2003) Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. II. High-density labeling of natural DNA. Nucleic Acids Res. 31, 2636-2646.
8. Arzumanov, A. A., Victorova, L. S., and Jasko, M. V. (2000) Synthesis of non-nucleoside triphosphate analogues, a new type of substrates for terminal deoxynucleotidyl transferase. Nucleosides, Nucleotides Nucleic Acids 19, 1787-1793.
9. Arzumanov, A. A., Victorova, L. S., Jasko, M. V., Yesipov, D. S., and Krayevsky, A. A. (2000) Terminal Deoxynucleotidyl Transferase Catalyzes the Reaction of DNA Phosphorylation. Nucleic Acids Res. 28, 1276-1281.
10. Khandazhinskaya, A. L., Kukhanova, M. K., and Jasko, M. V. (2005) New nonnucleoside substrates for terminal deoxynucleotidyl transferase: synthesis and the dependence of substrate properties on structure. Bioorg. Chem. (Russian) 31, 394-398.
11. Crespan, E., Zanoli, S., Khandazhinskaya, A., Shevelev, I., Jasko, M., Alexandrova, L., Kukhanova, M., Blanca, G, Villani, G., Hubscher, U., Spadari, S., and Maga, G. (2005) Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases beta and lambda. Nucleic Acids Res. 33, 4117-4127.
12. Langer, P. R., Waldrop, A. A., and Ward, D. C. (1981) Enzymatic synthesis of biotin-labeled polynucleotides: Novel nucleic acid affinity probes. Proc. Natl. Acad. Sci. U.S.A. 78, 6633-6637.
13. Alexandrova, L. A., Atrazhev, A. M., Kukhanova, M. K., and Krayevsky, A. A. (1987) Incorporation into DNA chain of fluorescent derivative 2′-deoxyuridilic acid at the catalysis by E. coli DNA polymerase. Bioorg. Chem. (Russian) 13, 643-647.
14. Becker, M., and Makela, O. (1975) Modification of bacteriophage with hapten-epsilon-aminocaproyl-N-hydroxysuccinimide esters. Immunochemistry 12, 329-331.
15. Sambrook, G., Fritch, E. F., and Manniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
16. Mityaeva, O. N., Nasedkina, T. V., Zharinov, V. S., Turygin, A. Yu., Chupeeva, V. V., Kreindlin, E. Yu., and Mirzabekov, A. D. (2004) Analysis of chromosome translocations involving MML by hybridization with an oligonucleotide microarray. Mol. Biol. (Mosk.) 38, 449-456.
17. Nasedkina, T. V., Zharinov, V. S., Isaeva, E. A., Mityaeva, O. N., Yurasov, R. N., Surzhikov, S. A., Turygin, A. Yu., Rubina, A. Yu., Karachunskii, A. I., Gartenhaus, R. B., and Mirzabekov, A. D. (2003) Clinical screening of gene rearrangements in childhood leukemia using a multiplex PCR-microarray approach. Clin. Cancer Res. 9, 5620-5629.
18. Rubina, A. Yu., Pan'kov, S. V., Dementieva, E. I., Pen'kov, D. N., Butygin, A. V., Vasiliskov, V. A., Chudinov, A. V., Mikcheikin, A. L., Mikhailovich, V. M., and Mirzabekov, A. D. (2004) Hydrogel drop microchip with immobilized DNA: properties and methods for large-scale production. Anal. Biochem. 325, 92-106.
19. Alexandrova, L. A., Skoblov, A. Yu., Jasko, M. V., Victorova, L. S., and Krayevsky, A. A. (1998) 2′-Deoxynucleoside 5′-triphosphates modified at α-, β- and γ-phosphates as substrates for DNA polymerases. Nucleic Acids Res. 26, 778-786.
20. Treibs, A., und Kreuzer, F. H. (1968) Difluorboryl-komlexe von Di- und Tripyrrylmethenen. Liebigs Ann. Chem. 718, 208-223.
21. 2 complexes as laser dyes: 1. Heteroatom Chem. 1, 389-399.
22. Fischer, H., and Orth, H. (1937) A. Zweikernige Pyrrolsysteme. In Die Chimie des Pyrrols, II Brand, pp 1-59, Leipzig Akademische Verlaggeselschaft, Pyrrolfarbstoffe, Leipzig.
23. Ogura, H., Kobayashi, T., Shimizu, K., Kawabe, K., and Takeda, K. (1979) A novel active ester synthesis reagent (N,N′-disuccinimidyl carbonate). Tetrahedron Lett. 49, 4745-4746.