Frac tionation of trichostatin a mechanism of action cells and isolation of the RTCs was per formed according to Fassati and Goff with modifications as described Inhibitors,Modulators,Libraries previously. Briefly, har vested cells were washed with cold PBS and homoge nized in cold hypotonic buffer supplemented with 0. 025% Brij 96 using EZ Grind kit. Viral RTCs Inhibitors,Modulators,Libraries were purified from total cell homogenates by centrifugation through a 50% sucrose cushion in hypotonic buffer at 100,000g in a Beck man MLS 50 rotor for 3 h at 4 C. Pelleted HIV 1 RTCs were resuspended in 200 ul of buffer K and stored at 80 C. DNA from RTC suspensions containing about 500 pg p24CA was extracted using the IsoQuick DNA Isolation kit with an addition of 25 ug of glycogen in each RTC sample. Quantitative PCR DNA from purified viral RTCs was analyzed by real time PCR using two sets of primers.

The first set detects the negative strand strong stop DNA and consists of forward primer M667 specific for the R U5 region of the HIV 1 LTR. The second set recognizes the positive strand DNA and consists of primers FOR LATE specific Inhibitors,Modulators,Libraries for the U5 �� LTR region. PCR reactions were performed with PerfeCTa qPCR FastMix, UNG using 300 nM of each primer and 200 nM probe. The conditions used were one cycle at 45 C for 2 min, and at 95 C for 4 min, then 15 sec at 95 C, and 30 sec at 60 C for 45 cycles. Serial dilutions of DNA from 8E5 cells were used as the quantitative standards. Quan titative analysis of 2 LTR circles was performed accord ing to published protocol. The 2 LTR standard was kindly provided by Michael Bukrinsky.

The Real time PCR assay was performed with forward primer Viral 2 LTR circles were detected from 500 ng total cellular DNA with PerfeCTa qPCR FastMix, UNG. Reaction conditions were the same as described above. Two step nested PCR assays were used for quantitative HIV 1 DNA Inhibitors,Modulators,Libraries integration analysis. The first round PCR was per formed in a 25 ul reaction mix as described previously. Briefly, 100 nM of the genomic Alu forward pri mer, and 100 ng of cellular genomic DNA were mixed with 1. 5 mM MgCl2, 0. 25 mM dNTPs, 0. 05 U of Platinum Taq DNA poly merase and Taq polymerase reaction buffer. The conditions were 2 min hot start at 94 C, then 30 sec at 93 C, 1 min at 50 C, and 2 min at 70 C for 20 cycles. The second round was performed with 5 ul of the material from the first round in 20 ul of reaction mix.

The primer set and reaction conditions were the same as for quantitative detection of the posi tive strand HIV 1 DNA described above. Serial dilutions of DNA from 8E5 cells were used to calculate the rela tive copy numbers of integrated DNA. Inhibitors,Modulators,Libraries To normalize integration data relative to target cell http://www.selleckchem.com/products/jq1.html DNA, a quantita tive real time PCR of b globin DNA was performed using the forward primer BGF1 Real time PCR reactions were carried out at least in triplicate using the iCycler with iQ Multicolor Real time PCR Detection System and iCycler software.