Journal: Nature communications

Article Title: Programmable multivalent display of receptor ligands using peptide nucleic acid nanoscaffolds.

doi: 10.1038/ncomms1629

Figure Lengend Snippet: Figure 2 | Chemical and cartoon representations of LK-PNA assembled onto DNA. (a) Chemical structure of LKγ-PNA bound to DNA. (b, c) Ribbon and cartoon diagrams of four LKγ-PNAs (each bearing one ligand) bound to a linear DNA.

Article Snippet: To make PNA:DNA complexes, a 1× PBS buffer solution of 20 μM DNA (Supplementary Table S1, Integrated DNA Technologies) was combined with the appropriate concentration of PNA conjugate depending on the repeat unit number on the DNA (ultraviolet quantification was performed using either a Nanodrop ND 1000, or an Agilent 8453 UV-Vis Spectrophotometer) at 25 °C.

Techniques:

Journal: Nature communications

Article Title: Programmable multivalent display of receptor ligands using peptide nucleic acid nanoscaffolds.

doi: 10.1038/ncomms1629

Figure Lengend Snippet: Figure 3 | Construction and screening of the DNA:PNA-Yx multivalent library. (a) Generation of the multivalent library by complexing each PNA in the first box with every DNA in the second box. PNA-A is an aegPNA oligomer with a c(RGDfK) bound to the N terminus. PNA-B, PNA-C and PNA-D have 1, 2 or 3 c(RGDfK) units, respectively, conjugated through γ-sidechains of internal LKγ-PNA residues. DNA is numbered according to how many complementary sequences each contains and represents the number of PNAs that would be complexed. Inhibition of C32 cell adhesion to vitronectin was examined with DNA:PNA complexes. (b) Three- dimensional representations of IC50 data from the screen of the library (A/B represents results from either PNA A or B). Data for DNA:PNA- C/D13 − 15 were not acquired because inhibitory activity was maximized at shorter lengths of ssDNA (see Supplementary Fig. S2 for error bars).

Article Snippet: To make PNA:DNA complexes, a 1× PBS buffer solution of 20 μM DNA (Supplementary Table S1, Integrated DNA Technologies) was combined with the appropriate concentration of PNA conjugate depending on the repeat unit number on the DNA (ultraviolet quantification was performed using either a Nanodrop ND 1000, or an Agilent 8453 UV-Vis Spectrophotometer) at 25 °C.

Techniques: Inhibition, Activity Assay

Journal: Nature communications

Article Title: Programmable multivalent display of receptor ligands using peptide nucleic acid nanoscaffolds.

doi: 10.1038/ncomms1629

Figure Lengend Snippet: Figure 4 | Atomic-scale computational model of an LK-PNA:DNA complex bound to V3 integrin receptors. (a, b) The side and top views of a molecular model of DNA:PNA-D1 bound to a cluster of three integrins (coloured in pewter). The DNA template is dark blue, the LKγ-PNA, including all bases and linkers, is sky blue, and c(RGDfK) residues are fuchsia.

Article Snippet: To make PNA:DNA complexes, a 1× PBS buffer solution of 20 μM DNA (Supplementary Table S1, Integrated DNA Technologies) was combined with the appropriate concentration of PNA conjugate depending on the repeat unit number on the DNA (ultraviolet quantification was performed using either a Nanodrop ND 1000, or an Agilent 8453 UV-Vis Spectrophotometer) at 25 °C.

Techniques:

Journal: Nature communications

Article Title: Programmable multivalent display of receptor ligands using peptide nucleic acid nanoscaffolds.

doi: 10.1038/ncomms1629

Figure Lengend Snippet: Figure 5 | In vivo activity and determination of stoichiometry for LK-PNA:DNA complexes. (a) Displacement of 125I-Echistatin from integrin αVβ3 on C32 cells by c(RGDfK) and DNA:PNA-D5. Kd c(RGDfK) = 6.3×10 − 8 M; Kd DNA:PNA-D5 = 1.6×10 − 10 M. Error bars represent 2 s.d. (n = 3). (b) The effect of DNA:PNA-D5 on metastatic potential of B16F10 cells based on the tumour development in C57BL/6NCr mice. All mice were injected with 5×105 B16F10 cells. Error bars represent 1 s.d. (n = 8 mice). (c) Lungs of killed mice after fixation with tumour lesions indicated by dark spots. The mice treated with DNA: PNA-D5 had visibly fewer tumour colonies present after 14 days compared with the control or c(RGDfK) alone. Each row corresponds to three mice out of a group of eight. (d) Absorbance c(s) distributions obtained from sedimentation velocity data collected at 50 krpm and 20 °C for DNA:PNA-B5 at loading concentrations of 0.35 (blue), 0.78 (red) and 1.47 (green) A260. The complex was prepared using a slight excess of PNA seen at ~1.0 S.

Article Snippet: To make PNA:DNA complexes, a 1× PBS buffer solution of 20 μM DNA (Supplementary Table S1, Integrated DNA Technologies) was combined with the appropriate concentration of PNA conjugate depending on the repeat unit number on the DNA (ultraviolet quantification was performed using either a Nanodrop ND 1000, or an Agilent 8453 UV-Vis Spectrophotometer) at 25 °C.

Techniques: In Vivo, Activity Assay, Injection, Control, Sedimentation