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| 1. |
Maeda, K., Das, D., Yin, P.D., Tsuchiya, K., Ogata-Aoki, H., Nakata, H., Norman, R.B., Hackney, L.A., Takaoka, Y. and Mitsuya, H.
(2008)
Involvement of the second extracellular loop and transmembrane residues of CCR5 in inhibitor binding and HIV-1 fusion: Insights into the mechanism of allosteric inhibition.
J. Mol. Biol.
381
,
956–74
.
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Notes:
The authors examined the role of specific amino acids within the second extracellular loop (ECL2) of C-C chemokine receptor 5 (CCR5), which is a coreceptor for human immunodeficiency virus type 1, in HIV-1-mediated cell fusion. The authors substituted single and multiple amino acids in ECL2 by site-directed mutagenesis, transfected MAGI cells with these CCR5 mutations, then monitored the effect of the mutations on the magnitude of cell-cell fusion. Their cell fusion assay used the pLTR-LucE plasmid, which encodes firefly luciferase and is transcriptionally activated by the HIV-1 tat protein. When tat+ cells fuse with pLTR-LucE+ cells, transcription of the luciferase gene is activated, and the level of luminescence becomes a measure of cell fusion. To peform the cell fusion assay, the researchers combined tat+, env+ 293T cells and pLTR-LucE+, CCR5+ MAGI cells for 6 hours, then measured luciferase activity using the Bright-Glo™ Luciferase Assay System. This assay allowed the researchers to identify amino acids within ECL2 that are involved in HIV-1-mediated cell fusion.
(0003971) |
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Products: Bright-Glo™ Luciferase Assay System |
| 2. |
Darnell GA, Schroder WA, Gardner J, Harrich D, Yu H, Medcalf RL, Warrilow D, Antalis TM, Sonza S, Suhrbier A.
(2007)
SerpinB2 is an inducible host factor involved in enhancing HIV-1 transcription and replication.
J. Biol. Chem.
281
,
31348-31358
.
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| |
Notes:
Expression of SerpinB2 by by activated monocytes and macrophages is up-regulated during inflammatory processes and following infection with certain parasitic, viral and bacterial pathogens. These authors identified SerpinB2 as a potentially important host factor in enhancing HIV transcription. They showed that HIV-1 infection and gp120 treatment of peripheral blood mononuclear cells caused induction of SerpinB2, and that SerpinB2 expression resulted in enhanced viral replication. Viral transcription was increased 3-10 fold in cells expressing SerpinB2 and was reduced in macrophages from SerpinB2 knockout mice. They used a series of truncated HIV-1 promoter constructs to localize the region associated with SerpinB2 enhancement of transcription to a region of the HIV-1 long terminal repeat promoter containing three Sp1 binding sites. They used luciferase reporter constructs and beta-galactosidase control vectors in these reporter assays.
(0003710) |
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Products: β-Galactosidase Enzyme Assay System with Reporter Lysis Buffer | pGL3-Basic Vector |
| 3. |
Küpfer, P.A., Crey-Desbiolles, C. and Leumann, C.J.
(2007)
Trans-lesion synthesis and RNaseH activity by reverse transcriptases on a true abasic RNA template.
Nucleic Acids Res.
35
,
6846–53
.
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Notes:
The authors investigated the effect of abasic RNA on DNA primer extension by various reverse transcriptase, including those from HIV-1, avian myeloblastosis virus (AMV) and Moloney muring leukemia virus (MMLV) and determined the preference of dNTP incorporation at abasic sites. The authors found that trans-lesion synthesis readily occurs with HIV-1 and to a lesser extent AMV RT, but MMLV RT aborts synthesis. The MMLV used in this study was M-MLV Reverse Transcriptase, RNAse H Minus, from Promega.
(0003909) |
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Products: M-MLV Reverse Transcriptase, RNase H Minus |
| 4. |
Stoddard, E, Cannon, G., Ni, H., Kariko, K. Capodici, J., Malamud, D., Weissman, D.
(2007)
gp340 expressed on human genital epithelia binds HIV-1 envelope protein and facilitates viral transmission.
J. Immunol.
179
,
3126-3132
.
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Notes:
The authors sought to identify the mediators of transmission of HIV across the mucosal barrier in humans. They noted that transmission occurs even the the genital tract epithelium is seemingly not damaged. In this study they showed that gp340 expressed on primary female genital epithelial cells binds HIV-1 and enhances transmission of otherwise subinfectious amounts of HIV to infect cells, also allowing transmission to occur over longer time periods. Their study methods included plating a variety of cell types, incubating these cells with HIV, and lysing the cells with Luciferase Cell Culture Lysis Reagent, then measuring HIV-1 p24 content by ELISA.
(0003701) |
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Products: Luciferase Cell Culture Lysis 5X Reagent |
| 5. |
Zhang, Z., Klatt, A., Henderson, A.J., and Gilmour, D.S.
(2007)
Transcription termination factor Pcf11 limits the processivity of Pol II on an HIV provirus to repress gene expression.
Genes Dev.
21
,
1609-1614
.
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Notes:
These authors showed that the termination factor Pcf11 negatively regulates expression of the HIV provirus by causing premature termination RNA pol II-mediated transcription elongation. ChIP assays revealed an association between Pcf11 and the HIV promoter region, and siRNA depletion of Pcf11 caused an increase in viral replication. Transcription in Pcf11-depleted nuclear extracts was shown to be insensitive to 6-dichloro-beta-D-ribofuranosylbenzimidazole (DRB), which is known to cause premature termination. Addition of purified Pcf11 back to the depleted nuclear extracts restored DRB sensitivity. The authors concluded that since HIV expression increases when Pcf11 is depleted, premature termination mediated by Pcf11 appears to play a role in maintaining transcriptional latency of the provirus.
(0003709) |
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Products: HeLaScribe® Nuclear Extract in vitro Transcription Grade | HeLaScribe® Nuclear Extract in vitro Transcription System |
| 6. |
Ramírez YJ, Tasciotti E, Gutierrez-Ortega A, Donayre Torres AJ, Olivera Flores MT, Giacca M, Gómez Lim MA.
(2007)
Fruit-specific expression of the human immunodeficiency virus type 1 Tat gene in tomato plants and its immunogenic potential in mice.
Clinical and Vaccine Immunology
14
,
685-692
.
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Notes:
In this study, the HIV Tat gene was expressed in tomato plants. Mice were given 10mg of tomato fruit extract from either transgenic or wild-type plants orally, intraperitoneally and intramuscularly. A strong anti-Tat immune response was obtained in mice immunized with the transgenic fruit, regardless of the administration route. Mice that received oral vaccination developed early evidence of mucosal immunity. Sera from the immunized mice inhibited Tat-dependent transactivation of the HIV long terminal repeat promoter in a luciferase reporter assay.
(0003706) |
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Products: Dual-Luciferase® Reporter Assay System | Dual-Luciferase® Reporter Assay System 10-Pack |
| 7. |
Betzi S, Restouin A, Opi S, Arold ST, Parrot I, Guerlesquin F, Morelli X, Collette Y.
(2007)
Protein protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef protein.
Proc. Natl. Acad. Sci. U S A
104
,
19256-19261
.
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Notes:
The authors wanted to screen inhibitory compounds for the HIV-1 accessory protein Nef using both computer modeling and experimental methods. Using a structure-based program for the SH3 binding surface of Nef, drug compounds were screened in silico and then further analyzed using a cell-based assay. The Nef gene and SH3 domain were cloned into the pACT and pBIND Vectors of the CheckMate™ Mammalian Two-Hybrid System, transfected into COS-7 cells, and 18 hours later, the cells exposed to potential inhibitors. After 24 hours, luciferase activity was assessed using either the Dual-Glo™ or the Steady-Glo® Luciferase Assay Systems.
(0003751) |
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Products: CheckMate™ Mammalian Two-Hybrid System | Dual-Glo® Luciferase Assay System | Steady-Glo® Luciferase Assay System |
| 8. |
Koh Y, Matsumi S, Das D, Amano M, Davis DA, Li J, Leschenko S, Baldridge A, Shioda T, Yarchoan R, Ghosh AK, Mitsuya H.
(2007)
Potent inhibition of HIV-1 replication by novel non-peptidyl small molecule inhibitors of protease dimerization.
J. Biol. Chem.
282
,
28709-28720
.
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Notes:
Dimerization of HIV-1 protease subunuts is essential for proteolytic activity and viral replication. These authors used a FRET assay to identify potential small molecule inhibitors of HIV-1 protease dimerization. After identifying a number of inhibitors in the FRET assay, they used the CheckMate™ Mammalian Two-Hybrid System to independently confirm the disruption of interaction between the two protein subunits.
(0003711) |
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Products: CheckMate™ Mammalian Two-Hybrid System |
| 9. |
Desfarages, S., San Filippo, J., Fournier, M. Calmels, C., Caumont-Sarcos, A., Litvak, S., Sung, P., Parissi, V.
(2006)
Chromosomal integration of LTR-flanked DNA in yeast expressing HIV-1 integrase: down regulation by RAD51
Nucleic Acids Res.
34
,
6215-6224
.
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Notes:
In the process of demonstrating the role of IN in HIV-1 integration in yeast, the authors purified all DNA vectors and PCR products with the Wizard® Plus SV Miniprep System and Wizard® SV Gel System. PCR products were generated using Taq DNA Polymerase. The pGEM®-T Vector was used to clone amplification products. Sequencing was performed using BamHI, religated with T4 DNA Ligase.
(0003704) |
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Products: BamHI | GoTaq® DNA Polymerase | pGEM®-T Vector System I | T4 DNA Ligase | Wizard® Plus SV Minipreps DNA Purification System | Wizard® SV Gel and PCR Clean-Up System |
| 10. |
Ji, C., Zhang, J., Cammack, N. and Sankuratri, S.
(2006)
Development of a novel dual CCR5-dependent and CXCR4-dependent cell-cell fusion assay system with inducible gp160 expression.
J. Biomol. Screen.
11
,
65–74
.
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Notes:
The effector cells of a high-throughput cell-cell fusion assay were dispensed in 384-well plates and expression of the envelope gene induced. Small-molecule compounds or antibodies being tested for their ability to prevent cell fusion were added to the effector cells (carrying firefly luciferase under control of HIV-2 LTR) prior to adding the target cells. The cells were cocultured for 20–24 hours, and luciferase expression was measured using the Steady-Glo® Luciferase Assay System.
(0003731) |
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Products: Steady-Glo® Luciferase Assay System |
| 11. |
Cavrois, M., Neidleman, J., Kreisberg, J.F., Fenard, D., Callebaut, C., and Greene, W.C.
(2006)
Human immunodeficiency virus fusion to dendritic cells declines as cells mature.
J. Virol.
80
,
1992–1999
.
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Notes:
To determine if fusion of the HIV virion to maturing dendritic cells (DCs) was the limiting step in HIV replication in DCs, β-lactamase-Vpr (BlaM-Vpr) chimeric virions were produced for use in a HIV virion fusion assay. To generate the virion chimeras, 293T cells were transfected with pNL4-3 or 81A proviral DNA, pCMV-BlaM-Vpr and pAdVAntage™ vectors. The virions were pseudotyped with various HIV env protein constructs. Forty-eight hours post-transfection, the virus-containing supernatant was harvested by centrifugation and normalized to p24 Gag content as measured by ELISA.
(0003495) |
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Products: pAdVAntage™ Vector |
| 12. |
Nguyen, D.G., Wolff, K.C., Yin, H., Caldwell, J.S. and Kuhen, K.L.
(2006)
"UnPAKing" Human Immunodeficiency Virus (HIV) replication: Using small interfering RNA screening to identify novel cofactors and elucidate the role of Group I PAKs in HIV infection
J. Virol.
80
,
130-7
.
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Notes:
The CellTiter-Glo® Luminescent Cell Viability Assay was used to assess viability of HeLaCD4βgal or U373-Magi-CCR5E cells transfected with siRNAs that targeted potential proviral host factors for HIV infection.
(0003374) |
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Products: CellTiter-Glo® Luminescent Cell Viability Assay |
| 13. |
Meschalchin, Alessdandra, Wünsche, W. Laufer, S.D., Grohmann, D., Restle, T., Sczakiel, G.
(2006)
Specific binding of a hexanuclotide to HIV-1 reverse transcriptase: a novel class of bioactive molecule.
Nucleic Acids Res.
34
,
5631-5637
.
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Notes:
The authors describe the highly specific binding of a hexanucleotide Hex-S3 to the large subunit of HIV-1 reverse transcriptase. They expressed the RTs of various HIV strains and equine infectious anemia virus RT, as well as the p51 subunit of HIV-1 RT, in E. coli, then purified the enzyme. Enzyme concentrations were determined using an extinction coefficient at 280nm of 140000 M-1 cm-1. All RTs studied were determined to be free of nuclease contamination. The authors then studied the binding of a variety of hexanucleotides to these RTs.
(0003702) |
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Products: Bovine Serum Albumin, Acetylated |
| 14. |
Goffin, V., Demonté, D., Vanhulle, C., de Walque, S., de Launoit, Y., Burny, A., Collette, Y., Van Lint, C.
(2005)
Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for viral infectivity.
Nucleic Acids Res.
33
,
4285-4310
.
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Notes:
A fragment containing HIV-1 LAI 5' LTR was cloned into the unique EcoICRI-XhoI site of the pGL3-Basic Reporter Vector. The Luciferase Reporter Assay was used to analyze DNA transfected cells for luciferase activity. The pRL-TK Vector was used as a transfection efficiency internal control with a Renilla cDNA under control of HSV-TK. Firefly luciferase activity derived from the HIV-1 LTR was normalized to the Renilla luciferase activities using the Dual-Luciferase® Reporter Assay.
(0003703) |
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Products: Dual-Luciferase® Reporter Assay System | Luciferase Assay System | pGL3-Basic Vector | pRL-TK Vector |
| 15. |
Wang, Y., Klock,H., Yin, H., Wolff, K., Bieza, K., Niswonger, K., Matzen, J., Gunderson, D., Hale, J, Lesley, S., Kuhen, K., Caldwell, J, Brinker, A.
(2005)
Homogeneous high-throughput screening assays for HIV-1 integrase 3' processing and strand transfer activities
J. Biomol. Screen.
10
,
456-462
.
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Notes:
HIV-1 integrase (HIV-IN) catalyzes a two-step reaction that results in HIV-1 provirus incorporation into the host cell genome. The steps involve an endonucleolytic 3’-processing (3P) followed by a strand transfer (ST) reaction. In past research it has been demonstrated that small molecule inhibitors of the in vitro activity of the 3P reaction only, lack antiviral activity, while inhibition of the HIV-IN ST reaction has been shown to be the key to effective suppression of viral replication in vivo. In the ST inhibitor realm, two series of diketo acids and naphthridine carboxamides have demonstrated antiviral activity in cell culture-based models. However, no compounds have completed clinical trials so far, due to either limited potency or high toxicity. Traditional integrase assays have been low-throughput, gel-based assays involving radiolabeled oligonucleotides. More recently high-throughput assays have been developed, but these microtiter-based assays, while amenable to automation, are complicated and labor intensive due to the need for plate coating and washing. The authors describe development of two robust, homogeneous time-resolved fluorescent energy transfer (TR-FRET)-based assays for HIV-IN 3P and ST reactions that are optimized for 384-well amd 1536-well plate formats. A screen for HIV-IN inhibitors was performed on a 1.36 x 106 compound library, resulting in a series of novel HIV-IN inhibitors that preferentially block integrase ST activity and show potential for further development as new antiviral drugs.
(0003776) |
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Products: Bright-Glo™ Luciferase Assay System |
| 16. |
Roisin A., Robin J.P., Dereuddre-Bosquet N., Vitte A.L., Dormont D., Clayette P. and Jalinot P.
(2004)
Inhibition of HIV-1 replication by cell-penetrating peptides binding Rev.
J. Biol. Chem.
279(10)
,
9208-14
.
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Notes:
The authors constructed a library of random heptapeptides using biotin-labeled sense and antisense oligonucleotides. The oligos were then hybridized, filled in with Klenow and cut with BamH I and Xma I, the restriction sites engineered into the oligo ends. Subsequently, the biotinylated ends were removed by incubation with Streptavidin MagneSphere® Paramagnetic Particles. Unbound fragments were then ligated upstream of the HIV-1 Tat protein transduction domain and the resultant plasmid transformed into bacteria for propagation.
(0003079) |
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Products: Streptavidin MagneSphere® Paramagnetic Particles |
| 17. |
Audige, A., Schlaepfer, E., Bonanomi, A., Joller, H., Knuchel, M.C., Weber, M., Nadal, D. and Speck, R.F.
(2004)
HIV-1 does not provoke alteration of cytokine gene expression in lymphoid tissue after acute infection ex vivo.
J. Immunol.
172
,
2687-2696
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Notes:
The authors used real-time quantitative PCR to characterize cytokine response after HIV infection of human lymphoid tissues. To synthesize first-strand cDNA, total RNA was reverse transcribed using the ImProm-II™ Reverse Transcription System: 200U of ImProm-II Reverse Transcriptase, 2µg of total RNA, 500ng of oligo(dT) primer, 500µM dNTPs 3mM MgCl2 and 24U of RNase inhibitor in 1x ImProm-II™ reaction buffer. To obtain viral stocks for infection, 293T cells were transfected with the proviral plasmids pNL4-3 and pYU-2 using the ProFection® Mammalian Transfection System—Calcium Phosphate.
(0003455) |
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Products: ImProm-II™ Reverse Transcriptase | ImProm-II™ Reverse Transcription System | ProFection® Mammalian Transfection System—Calcium Phosphate |
| 18. |
Ahmad, R., Sindhu, S.T., Toma, E., Morisset, R. and Ahmad, A.
(2003)
Elevated levels of circulating interleukin-18 in human immunodeficiency virus-infected individuals: Role of peripheral blood mononuclear cells and implications for AIDS pathogenesis.
J. Virol.
76
,
12448-12456
.
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Notes:
Serum was collected from HIV-1 infected patients and analyzed for total TGFß1 after acid treatment using the TGFß1 Emax® ImmunoAssay System.
(0002813) |
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Products: TGFβ1 Emax® ImmunoAssay System |
| 19. |
Lin, P.F., Blair, W., Wang, T., Spicer, T., Guo, Q., Zhou, N., Gong, Y.F., Wang, H.G., Rose, R., Yamanaka, G., Robinson, B., Li, C.B., Fridell, R., Deminie, C., Demers, G., Yang, Z., Zadjura, L., Meanwell, N. and Colonno, R.
(2003)
A small molecule HIV-1 inhibitor that targets the HIV-1 envelope and inhibits CD4 receptor binding.
Proc. Natl. Acad. Sci. U S A
100(19)
,
11013-11018
.
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Notes:
To test the effect of BMS-378806, a new small molecule inhibitor of HIV-1, a cell fusion assay was developed. Target cells that stably expressed CD4, CXCR4 or CCR5 receptors and carry a responsive luciferase plasmid were prepared. Effector cells were transiently transfected with HIV coat protein gp160 from various strains of virus, and a plasmid to activate the responsive element promoting luciferase. Therefore, if the cells fuse, luciferase is activated. To measure this activation, effector cells were plated with target cells in a 1:2 ratio and seeded into 96-well plates at 1.5 x 104 cells/well and incubated with various concentrations of BMS-378806 for 12-24 hours. Luciferase activity was determined with the Steady-Glo® Reagent.
(0002737) |
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Products: Luciferase Assay System | Steady-Glo® Luciferase Assay System |
| 20. |
Lee-Huang, S., Huang, P.L., Sun, Y., Huang, P.L., Kung, H-F., Blithe, D. L., Chen, H-C.
(1999)
Lysozyme and RNases as anti-HIV components in β-core preparations of human chorionic gonadotropin
Proc. Natl. Acad. Sci. U S A
96
,
2678-2681
.
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Notes:
The authors used the CellTiter 96® AQueous Non-Radioactive Cell Proliferation Assay to determine whether cell viability of chronically HIV-infected ACH-2 lymphocytes and U1 monocytes was affected by anti-viral lysozyme and anti-viral RNase obtained from human chorionic gonadotropin preparations.
(0002477) |
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Products: CellTiter 96® AQueous Non-Radioactive Cell Proliferation Assay |
| 21. |
de Haard, H.J.W., Kazemier, B., Koolen, M.J.M., Nijholt, L.J., Meloen, R.H., van Gemen, B., Hoogenboom, H.R., Arends, J.-W.
(1998)
Selection of recombinant, library-derived antibody fragments against p24 for human immunodefiency virus type 1 diagnostics.
Clin. Diagn. Lab. Immunol.
5
,
636-644.
.
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Notes:
The Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) were used to select single-chain Fv (scFv) fragments capable of binding the major HIV-1 capsid protein, p24. The library was constructed and expressed scFv fragments were screened for their interaction with biotinylated p24. The scFv were either reacted with biotinylated p24 in solution then captured with SA-PMPs for analysis or reacted with the biotinylated p24 already captured on the SA-PMPs. The panning method resulted in a 100 fold enrichment for the soluble interaction then capture and a 10,000-fold enrichment with precaptured complexes.
(0001260) |
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Products: Streptavidin MagneSphere® Paramagnetic Particles |
| 22. |
Cara, A., Rybak, S.M., Newton, D.L., Rottschafer, S.E., Reitz Jr., M.S., and Gusella, G.L.
(1998)
Inhibition of HIV-1 replication by combined expression of gag dominant negative mutant and a human ribonuclease in a tightly controlled HIV-1 inducible vector
Gene Ther.
5
,
65-75
.
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Notes:
The ProFection® Mammalian Transfection System - Calcium Phosphate was used to transfect HeLa and HeLa-Tat cell lines. The authors developed a vector-antiviral gene system for use in gene therapy in the treatment of HIV-1. pGEM®-luc was used as a negative control in luciferase assays of transfected cells.
(0001388) |
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Products: Luciferase Assay System | pGEM®-luc DNA | ProFection® Mammalian Transfection System—Calcium Phosphate |
| 23. |
Garcia-Martinez, L. F. , Ivanov, D. , Gaynor, R. B.
(1997)
Association of Tat with purified HIV-1 and HIV-2 transcription preinitiation complexes.
J. Biol. Chem.
272
,
6951-6958
.
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Notes:
HIV transcription complexes were analyzed by gel filtration chromatography and western blotting of fractions with the Anti-TFIID mAb. The recombinant TFIID was used as a control.
(0001141) |
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| 24. |
Rucker, J., Samson, M., Doranz, B.J., Libert, F., Berson, J.F., Yi, Y., Smyth, R. J., Collman, R.G., Broder, C.C., Vassart, G., Doms, R.W., Parmentier, M.
(1996)
Regions in beta-chemokine receptors CCR5 and CCR2b that determine HIV-1 cofactor specificity.
Cell
87
,
437-446
.
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Notes:
The Luciferase T7 Control DNA from the TNT® Coupled Reticulocyte Lysate System was used to look at cofactors to CD4 necessary for entry of HIV-1. HeLa cells were infected with recombinant vaccinia virus vectors expressing the protein of interest and the T7 RNA Polymerase. Quail QT6 cells were transfected with plasmids encoding CD4, the desired cofactor, and the Luciferase T7 Control DNA. Fusion of the two cells was then quantitated by luciferase activity.
(0000462) |
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Products: TNT® T7 Coupled Reticulocyte Lysate System |
| 25. |
Hilfinger, J.M., Clark, N., Smith, M., Robinson, K. and Markovitz, D.M.
(1993)
Differential regulation of the human immunodeficiency virus type 2 enhancer in monocytes at various stages of differentiation.
J. Virol.
67
,
4448-4453
.
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Notes:
Pu.1, the macrophage- and B-cell-specific ets-related transcription factor, was synthesized using the TNT® T7 Coupled Reticulocyte Lysate System. In electrophoretic mobility shift assays Pu.1 binds to PuB2, one of two purine-rich binding sites in the HIV-2 enhancer.
(0001803) |
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Products: TNT® T7 Coupled Reticulocyte Lysate System | TNT® T7 Coupled Reticulocyte Lysate System, Trial Size |