Oint (0, 12, 24, 48, and 72 hours) and immediately stored at 280uC to minimize unnecessary degradation. Samples were then subjected to 12 denaturing polyacrylamide gel electrophoresis (PAGE). The band density was quantitatively measured using gel densitometry and analyzed using gene tools software from Syngene.Circular Dichroism (CD) SpectroscopyTo deduce the structure of PS-modified SL2-B aptamer, 10 mM of FCCP chemical information aptamer was dissolved in the PBS buffer for CD analysis. The CD spectrum was recorded in wavelength range of 200?20 nm at two different temperatures 25uC and 37uC and the data 
were the average of 10 scans. The CD spectrum analysis was performed using cuvette 12926553 of 1-cm path length on a Jasco J-810 spectropolarimeter. The PBS buffer was used as blank for both the temperatures and the spectral data for SL2-B aptamer was blank corrected.HDAC-IN-3 cost antiproliferative Activity AssayHep G2 and MCF-7 cells were seeded at a density of 2000 cells/ ml and HCT-116 cells were seeded at a density of 3000 cells/ml in 96-well plate at day 0 in DMEM media supplemented with 10 FBS and penicillin/streptomycin mixture. SL2-B aptamer (unmodified/PS-modified) and scrambled aptamer were incubated with cells at different concentrations and incubated for 3 days in hypoxia conditions (5 CO2, 1 O2, and 94 N2) inside theAntiproliferative Activity of Aptamer on CancerFigure 1. Typical SPR sensorgrams demonstrating interaction of aptamer with immobilized VEGF165 protein at different concentration (bottom to top, 0.2 to 100 nM). Point A to B corresponds to association phase and point B to C corresponds to the dissociation phase 
in all the sensorgrams. Shown here is PS-modified SL2-B aptamer (Kd = 0.5660.44 nM). doi:10.1371/journal.pone.0050964.ghypoxia chamber. The cell medium was not changed for 3 days. No cell transfecting or permeabilizing agent was added. The antiproliferative effect of aptamer on the cells was determined by measuring cell viability using colorimetric MTT assay. The optical density reading was recorded using microplate reader (Tecan, infinite M200) at 570 nm with background subtraction at 620 nm. The experiment was performed in triplicates.Apoptosis AssayAnnexin V apoptosis assay was performed to investigate the cell death mechanism in Hep G2 cells according to manufacturer’s protocol. Cells were harvested by trypsinization and washed twice with cold PBS (1X) and subsequently stained with FITC Annexin V and propidium iodide. Analysis was 1516647 performed on the BeckmanCouter CyAnTM ADP flow cytometer by counting 15000 events.Microscopy ImagingThe antiproliferative effect of PS-modified SL2-B aptamer on Hep G2 cells was assessed using optical microscopic imaging. Same conditions were maintained as for the antiproliferative activity assay and cells were imaged after 72 hours of aptamer treatment. Photomicrographs were taken on an Eclipse T5000 (Nikon, Japan) light microscope with Tame2u acquisition software.Flow Cytometry AnalysisFlow cytometry was used to study the effect of PS-modified SL2B aptamer on Jagged-1 protein expression in Hep G2 cells. Hep G2 cells were seeded at a density of 80,000 cells/ml in 6-well plate at day 0 in DMEM media supplemented with 10 FBS and penicillin/streptomycin mixture. Following day after seeding, the cells were treated with modified SL2-B aptamer and scrambledTable 1. Unmodified and PS-modified SL2-B aptamer sequences along with their equilibrium dissociation constant (Kd) values determined using surface plasmon resonance (SP.Oint (0, 12, 24, 48, and 72 hours) and immediately stored at 280uC to minimize unnecessary degradation. Samples were then subjected to 12 denaturing polyacrylamide gel electrophoresis (PAGE). The band density was quantitatively measured using gel densitometry and analyzed using gene tools software from Syngene.Circular Dichroism (CD) SpectroscopyTo deduce the structure of PS-modified SL2-B aptamer, 10 mM of aptamer was dissolved in the PBS buffer for CD analysis. The CD spectrum was recorded in wavelength range of 200?20 nm at two different temperatures 25uC and 37uC and the data were the average of 10 scans. The CD spectrum analysis was performed using cuvette 12926553 of 1-cm path length on a Jasco J-810 spectropolarimeter. The PBS buffer was used as blank for both the temperatures and the spectral data for SL2-B aptamer was blank corrected.Antiproliferative Activity AssayHep G2 and MCF-7 cells were seeded at a density of 2000 cells/ ml and HCT-116 cells were seeded at a density of 3000 cells/ml in 96-well plate at day 0 in DMEM media supplemented with 10 FBS and penicillin/streptomycin mixture. SL2-B aptamer (unmodified/PS-modified) and scrambled aptamer were incubated with cells at different concentrations and incubated for 3 days in hypoxia conditions (5 CO2, 1 O2, and 94 N2) inside theAntiproliferative Activity of Aptamer on CancerFigure 1. Typical SPR sensorgrams demonstrating interaction of aptamer with immobilized VEGF165 protein at different concentration (bottom to top, 0.2 to 100 nM). Point A to B corresponds to association phase and point B to C corresponds to the dissociation phase in all the sensorgrams. Shown here is PS-modified SL2-B aptamer (Kd = 0.5660.44 nM). doi:10.1371/journal.pone.0050964.ghypoxia chamber. The cell medium was not changed for 3 days. No cell transfecting or permeabilizing agent was added. The antiproliferative effect of aptamer on the cells was determined by measuring cell viability using colorimetric MTT assay. The optical density reading was recorded using microplate reader (Tecan, infinite M200) at 570 nm with background subtraction at 620 nm. The experiment was performed in triplicates.Apoptosis AssayAnnexin V apoptosis assay was performed to investigate the cell death mechanism in Hep G2 cells according to manufacturer’s protocol. Cells were harvested by trypsinization and washed twice with cold PBS (1X) and subsequently stained with FITC Annexin V and propidium iodide. Analysis was 1516647 performed on the BeckmanCouter CyAnTM ADP flow cytometer by counting 15000 events.Microscopy ImagingThe antiproliferative effect of PS-modified SL2-B aptamer on Hep G2 cells was assessed using optical microscopic imaging. Same conditions were maintained as for the antiproliferative activity assay and cells were imaged after 72 hours of aptamer treatment. Photomicrographs were taken on an Eclipse T5000 (Nikon, Japan) light microscope with Tame2u acquisition software.Flow Cytometry AnalysisFlow cytometry was used to study the effect of PS-modified SL2B aptamer on Jagged-1 protein expression in Hep G2 cells. Hep G2 cells were seeded at a density of 80,000 cells/ml in 6-well plate at day 0 in DMEM media supplemented with 10 FBS and penicillin/streptomycin mixture. Following day after seeding, the cells were treated with modified SL2-B aptamer and scrambledTable 1. Unmodified and PS-modified SL2-B aptamer sequences along with their equilibrium dissociation constant (Kd) values determined using surface plasmon resonance (SP.