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Volumn 89, Issue 12, 2008, Pages 3119-3125

Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE; SHORT HAIRPIN RNA; POL PROTEIN; PROTEINASE; REVERSE TRANSCRIPTASE, HUMAN IMMUNODEFICIENCY VIRUS 1; RNA DIRECTED DNA POLYMERASE; UNCLASSIFIED DRUG; VIRUS RNA;

EID: 58149390387     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/vir.0.2008/003418-0     Document Type: Article
Times cited : (14)

References (45)
  • 1
    • 0035965239 scopus 로고    scopus 로고
    • The kissing hairpin sequence promotes recombination within the HIV-I 5′ leader region
    • Balakrishnan, M., Fay, P. J. & Bambara, R. A. (2001). The kissing hairpin sequence promotes recombination within the HIV-I 5′ leader region. J Biol Chem 276, 36482-36492.
    • (2001) J Biol Chem , vol.276 , pp. 36482-36492
    • Balakrishnan, M.1    Fay, P.J.2    Bambara, R.A.3
  • 2
    • 0344406983 scopus 로고    scopus 로고
    • Template dimerization promotes an acceptor invasion-induced transfer mechanism during human immunodeficiency virus type 1 minus-strand synthesis
    • Balakrishnan, M., Roques, B. P., Fay, P. J. & Bambara, R. A. (2003). Template dimerization promotes an acceptor invasion-induced transfer mechanism during human immunodeficiency virus type 1 minus-strand synthesis. J Virol 77, 4710-4721.
    • (2003) J Virol , vol.77 , pp. 4710-4721
    • Balakrishnan, M.1    Roques, B.P.2    Fay, P.J.3    Bambara, R.A.4
  • 3
    • 0034903425 scopus 로고    scopus 로고
    • Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription
    • Berkhout, B., Vastenhouw, N. L., Klasens, B. I. & Huthoff, H. (2001). Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription. RNA 7, 1097-1114.
    • (2001) RNA , vol.7 , pp. 1097-1114
    • Berkhout, B.1    Vastenhouw, N.L.2    Klasens, B.I.3    Huthoff, H.4
  • 4
    • 0034623018 scopus 로고    scopus 로고
    • Effect of ignoring the time of HIV seroconversion in estimating changes in survival over calendar time in observational studies: Results from CASCADE
    • CASCADE Collaboration
    • CASCADE Collaboration (2000). Effect of ignoring the time of HIV seroconversion in estimating changes in survival over calendar time in observational studies: results from CASCADE. AIDS 14, 1899-1906.
    • (2000) AIDS , vol.14 , pp. 1899-1906
  • 6
    • 0018304892 scopus 로고
    • Structure, replication, and recombination of retrovirus genomes: Some unifying hypotheses
    • Coffin, J. M. (1979). Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. J Gen Virol 42, 1-26.
    • (1979) J Gen Virol , vol.42 , pp. 1-26
    • Coffin, J.M.1
  • 7
    • 0028952146 scopus 로고
    • HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy
    • Coffin, J. M. (1995). HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267, 483-489.
    • (1995) Science , vol.267 , pp. 483-489
    • Coffin, J.M.1
  • 8
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding, Y., Chan, C. Y. & Lawrence, C. E. (2004). Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32, W135-W141.
    • (2004) Nucleic Acids Res , vol.32
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 9
    • 4043079959 scopus 로고    scopus 로고
    • Identification of a preferred region for recombination and mutation in HIV-1 gag
    • Dykes, C., Balakrishnan, M., Planelles, V., Zhu, Y., Bambara, R. A. & Demeter, L. M. (2004). Identification of a preferred region for recombination and mutation in HIV-1 gag. Virology 326, 262-279.
    • (2004) Virology , vol.326 , pp. 262-279
    • Dykes, C.1    Balakrishnan, M.2    Planelles, V.3    Zhu, Y.4    Bambara, R.A.5    Demeter, L.M.6
  • 10
    • 23144449384 scopus 로고    scopus 로고
    • Mechanistic features of recombination in HIV
    • Galetto, R. & Negroni, M. (2005). Mechanistic features of recombination in HIV. AIDS Rev 7, 92-102.
    • (2005) AIDS Rev , vol.7 , pp. 92-102
    • Galetto, R.1    Negroni, M.2
  • 11
    • 33646374954 scopus 로고    scopus 로고
    • Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle
    • Galetto, R., Giacomoni, V., Veron, M. & Negroni, M. (2006). Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle. J Biol Chem 281, 2711-2720.
    • (2006) J Biol Chem , vol.281 , pp. 2711-2720
    • Galetto, R.1    Giacomoni, V.2    Veron, M.3    Negroni, M.4
  • 13
    • 0025216861 scopus 로고
    • Retroviral recombination during reverse transcription
    • Goodrich, D. W. & Duesberg, P. H. (1990). Retroviral recombination during reverse transcription. Proc Natl Acad Sci U S A 87, 2052-2056.
    • (1990) Proc Natl Acad Sci U S A , vol.87 , pp. 2052-2056
    • Goodrich, D.W.1    Duesberg, P.H.2
  • 14
    • 0033563463 scopus 로고    scopus 로고
    • Automatic detection of conserved base pairing patterns in RNA virus genomes
    • Hofacker, I. L. & Stadler, P. F. (1999). Automatic detection of conserved base pairing patterns in RNA virus genomes. Comput Chem 23, 401-414.
    • (1999) Comput Chem , vol.23 , pp. 401-414
    • Hofacker, I.L.1    Stadler, P.F.2
  • 16
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker, I. L., Fekete, M. & Stadler, P. F. (2002). Secondary structure prediction for aligned RNA sequences. J Mol Biol 319, 1059-1066.
    • (2002) J Mol Biol , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 17
    • 0025635705 scopus 로고
    • Retroviral recombination and reverse transcription
    • Hu, W. S. & Temin, H. M. (1990). Retroviral recombination and reverse transcription. Science 250, 1227-1233.
    • (1990) Science , vol.250 , pp. 1227-1233
    • Hu, W.S.1    Temin, H.M.2
  • 18
    • 0033977268 scopus 로고    scopus 로고
    • High rate of recombination throughout the human immunodeficiency virus type 1 genome
    • Jetzt, A. E., Yu, H., Klarmann, G. J., Ron, Y., Preston, B. D. & Dougherty, J. P. (2000). High rate of recombination throughout the human immunodeficiency virus type 1 genome. J Virol 74, 1234-1240.
    • (2000) J Virol , vol.74 , pp. 1234-1240
    • Jetzt, A.E.1    Yu, H.2    Klarmann, G.J.3    Ron, Y.4    Preston, B.D.5    Dougherty, J.P.6
  • 19
    • 0000333554 scopus 로고    scopus 로고
    • Evidence for a unique mechanism of strand transfer from the transactivation response region of HIV-1
    • Kim, J. K., Palaniappan, C., Wu, W., Fay, P. J. & Bambara, R. A. (1997). Evidence for a unique mechanism of strand transfer from the transactivation response region of HIV-1. J Biol Chem 272, 16769-16777.
    • (1997) J Biol Chem , vol.272 , pp. 16769-16777
    • Kim, J.K.1    Palaniappan, C.2    Wu, W.3    Fay, P.J.4    Bambara, R.A.5
  • 20
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knudsen, B. & Hein, J. (2003). Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31, 3423-3428.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 21
    • 0028046638 scopus 로고
    • Genetic differences between blood- and brain-derived viral sequences from human immuno-deficiency virus type 1-infected patients: Evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences
    • Korber, B. T., Kunstman, K. J., Patterson, B. K., Furtado, M., McEvilly, M. M., Levy, R. & Wolinsky, S. M. (1994). Genetic differences between blood- and brain-derived viral sequences from human immuno-deficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences. J Virol 68, 7467-7481.
    • (1994) J Virol , vol.68 , pp. 7467-7481
    • Korber, B.T.1    Kunstman, K.J.2    Patterson, B.K.3    Furtado, M.4    McEvilly, M.M.5    Levy, R.6    Wolinsky, S.M.7
  • 22
    • 33144467988 scopus 로고    scopus 로고
    • Pausing during reverse transcription increases the rate of retroviral recombination
    • Lanciault, C. & Champoux, J. J. (2006). Pausing during reverse transcription increases the rate of retroviral recombination. J Virol 80, 2483-2494.
    • (2006) J Virol , vol.80 , pp. 2483-2494
    • Lanciault, C.1    Champoux, J.J.2
  • 23
    • 33751249244 scopus 로고    scopus 로고
    • HIV-1 subtype and circulating recombinant form (CRF) reference sequences
    • Los Alamos National Laboratory, NM, USA
    • Leitner, T., Korber, B., Daniels, M., Calef, C. & Foley, B. (2005). HIV-1 subtype and circulating recombinant form (CRF) reference sequences. In HIV Sequence Compendium. Los Alamos National Laboratory, NM, USA.
    • (2005) HIV Sequence Compendium
    • Leitner, T.1    Korber, B.2    Daniels, M.3    Calef, C.4    Foley, B.5
  • 25
    • 0032889281 scopus 로고    scopus 로고
    • Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination
    • Lole, K. S., Bollinger, R. C., Paranjape, R. S., Gadkari, D., Kulkarni, S. S., Novak, N. G., Ingersoll, R., Sheppard, H. W. & Ray, S. C. (1999). Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73, 152-160.
    • (1999) J Virol , vol.73 , pp. 152-160
    • Lole, K.S.1    Bollinger, R.C.2    Paranjape, R.S.3    Gadkari, D.4    Kulkarni, S.S.5    Novak, N.G.6    Ingersoll, R.7    Sheppard, H.W.8    Ray, S.C.9
  • 26
    • 0141730444 scopus 로고    scopus 로고
    • In vivo characteristics of human immunodeficiency virus type 1 intersubtype recombination: Determination of hot spots and correlation with sequence similarity
    • Magiorkinis, G., Paraskevis, D., Vandamme, A. M., Magiorkinis, E., Sypsa, V. & Hatzakis, A. (2003). In vivo characteristics of human immunodeficiency virus type 1 intersubtype recombination: determination of hot spots and correlation with sequence similarity. J Gen Virol 84, 2715-2722.
    • (2003) J Gen Virol , vol.84 , pp. 2715-2722
    • Magiorkinis, G.1    Paraskevis, D.2    Vandamme, A.M.3    Magiorkinis, E.4    Sypsa, V.5    Hatzakis, A.6
  • 27
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288, 911-940.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 28
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill, J. S. (1990). The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 29
    • 0035883822 scopus 로고    scopus 로고
    • The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination
    • Moumen, A., Polomack, L., Roques, B., Buc, H. & Negroni, M. (2001). The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination. Nucleic Acids Res 29, 3814-3821.
    • (2001) Nucleic Acids Res , vol.29 , pp. 3814-3821
    • Moumen, A.1    Polomack, L.2    Roques, B.3    Buc, H.4    Negroni, M.5
  • 30
    • 0037844873 scopus 로고    scopus 로고
    • Evidence for a mechanism of recombination during reverse transcription dependent on the structure of the acceptor RNA
    • Moumen, A., Polomack, L., Unge, T., Veron, M., Buc, H. & Negroni, M. (2003). Evidence for a mechanism of recombination during reverse transcription dependent on the structure of the acceptor RNA. J Biol Chem 278, 15973-15982.
    • (2003) J Biol Chem , vol.278 , pp. 15973-15982
    • Moumen, A.1    Polomack, L.2    Unge, T.3    Veron, M.4    Buc, H.5    Negroni, M.6
  • 31
    • 0036065416 scopus 로고    scopus 로고
    • Performance of an in-house genotypic antiretroviral resistance assay in patients pretreated with multiple human immunodeficiency virus type 1 protease and reverse transcriptase inhibitors
    • Peduzzi, C., Pierotti, P., Venturi, G., Romano, L., Mazzotta, F. & Zazzi, M. (2002). Performance of an in-house genotypic antiretroviral resistance assay in patients pretreated with multiple human immunodeficiency virus type 1 protease and reverse transcriptase inhibitors. J Clin Virol 25, 57-62.
    • (2002) J Clin Virol , vol.25 , pp. 57-62
    • Peduzzi, C.1    Pierotti, P.2    Venturi, G.3    Romano, L.4    Mazzotta, F.5    Zazzi, M.6
  • 32
    • 0029967721 scopus 로고    scopus 로고
    • HIV-1 dynamics in vivo: Virion clearance rate, infected cell life-span, and viral generation time
    • Perelson, A. S., Neumann, A. U., Markowitz, M., Leonard, J. M. & Ho, D. D. (1996). HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271, 1582-1586.
    • (1996) Science , vol.271 , pp. 1582-1586
    • Perelson, A.S.1    Neumann, A.U.2    Markowitz, M.3    Leonard, J.M.4    Ho, D.D.5
  • 33
    • 0024267430 scopus 로고
    • Fidelity of HIV-1 reverse transcriptase
    • Preston, B. D., Poiesz, B. J. & Loeb, L. A. (1988). Fidelity of HIV-1 reverse transcriptase. Science 242, 1168-1171.
    • (1988) Science , vol.242 , pp. 1168-1171
    • Preston, B.D.1    Poiesz, B.J.2    Loeb, L.A.3
  • 35
    • 0024273119 scopus 로고
    • The accuracy of reverse transcriptase from HIV-1
    • Roberts, J. D., Bebenek, K. & Kunkel, T. A. (1988). The accuracy of reverse transcriptase from HIV-1. Science 242, 1171-1173.
    • (1988) Science , vol.242 , pp. 1171-1173
    • Roberts, J.D.1    Bebenek, K.2    Kunkel, T.A.3
  • 37
    • 0037033049 scopus 로고    scopus 로고
    • Strand transfer occurs in retroviruses by a pause-initiated two-step mechanism
    • Roda, R. H., Balakrishnan, M., Kim, J. K., Roques, B. P., Fay, P. J. & Bambara, R. A. (2002). Strand transfer occurs in retroviruses by a pause-initiated two-step mechanism. J Biol Chem 277, 46900-46911.
    • (2002) J Biol Chem , vol.277 , pp. 46900-46911
    • Roda, R.H.1    Balakrishnan, M.2    Kim, J.K.3    Roques, B.P.4    Fay, P.J.5    Bambara, R.A.6
  • 38
    • 0027180278 scopus 로고
    • Retrovirus variation and reverse transcription: Abnormal strand transfers result in retrovirus genetic variation
    • Temin, H. M. (1993). Retrovirus variation and reverse transcription: abnormal strand transfers result in retrovirus genetic variation. Proc Natl Acad Sci U S A 90, 6900-6903.
    • (1993) Proc Natl Acad Sci U S A , vol.90 , pp. 6900-6903
    • Temin, H.M.1
  • 39
    • 30944461040 scopus 로고    scopus 로고
    • Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: An update
    • Thomson, M. M. & Nájera, R. (2005). Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: an update. AIDS Rev 7, 210-224.
    • (2005) AIDS Rev , vol.7 , pp. 210-224
    • Thomson, M.M.1    Nájera, R.2
  • 40
    • 0036319711 scopus 로고    scopus 로고
    • Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy
    • Thomson, M. M., Pérez-Alvarez, L. & Nájera, R. (2002). Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. Lancet Infect Dis 2, 461-471.
    • (2002) Lancet Infect Dis , vol.2 , pp. 461-471
    • Thomson, M.M.1    Pérez-Alvarez, L.2    Nájera, R.3
  • 41
    • 3843112243 scopus 로고    scopus 로고
    • HIV-1 subtype distribution and the problem of drug resistance
    • Wainberg, M. A. (2004). HIV-1 subtype distribution and the problem of drug resistance. AIDS 18 (Suppl. 3), S63-S68.
    • (2004) AIDS , vol.18 , Issue.SUPPL. 3
    • Wainberg, M.A.1
  • 43
    • 0033967743 scopus 로고    scopus 로고
    • Most retroviral recombinations occur during minus-strand DNA synthesis
    • Zhang, J., Tang, L. Y., Li, T., Ma, Y. & Sapp, C. M. (2000). Most retroviral recombinations occur during minus-strand DNA synthesis. J Virol 74, 2313-2322.
    • (2000) J Virol , vol.74 , pp. 2313-2322
    • Zhang, J.1    Tang, L.Y.2    Li, T.3    Ma, Y.4    Sapp, C.M.5
  • 44
    • 0036827628 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 recombination: Rate, fidelity, and putative hot spots
    • Zhuang, J., Jetzt, A. E., Sun, G., Yu, H., Klarmann, G., Ron, Y., Preston, B. D. & Dougherty, J. P. (2002). Human immunodeficiency virus type 1 recombination: rate, fidelity, and putative hot spots. J Virol 76, 11273-11282.
    • (2002) J Virol , vol.76 , pp. 11273-11282
    • Zhuang, J.1    Jetzt, A.E.2    Sun, G.3    Yu, H.4    Klarmann, G.5    Ron, Y.6    Preston, B.D.7    Dougherty, J.P.8
  • 45
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1


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