1
Yield was 38% in three steps. H NMR (400 MHz, DMSO-
131.8, 127.98, 127.43, 125.6, 125.5, 124.7, 120.5, 116.7, 86.7, 83.2,
78.5, 65.7, 65.5, 55.3, 52.41, 52.39, 49.9, 47.9, 47.3, 47.2, 42.9,
36.96, 36.8, 32.5, 32.0, 29.8, 29.5, 28.7, 28.4, 28.0, 27.98, 26.2,
19.4, 18.0, 18.0, 12.7. HRMS for [M+H]+ Calc: 1004.4677, found:
1004.4677.
d6) d (two rotamers) 11.43 (s, 1H), 8.58–8.50 (m, 1H), 7.86–7.80
(m, 2H), 7.64–7.61 (m, 2H), 7.40–7.25 (m, 4H), 4.25 (m, 3H),
2.75–3.67 (m, 2H), 3.55–3.42 (m, 5H), 3.15–3.10 (m, 2H), 2.55–
2.54 (m, 1H), 2.45–2.42 (m, 1H), 1.42&1.40&1.34&1.33 (4 s, 18H)
13C NMR (100 MHz, DMSO-d6) d (two rotamers) 172.3, 163.6,
156.52, 156.5, 152.3, 144.3, 143.0, 141.1, 139.9, 137.9, 129.4, 127.7,
127.3, 125.7, 129.4, 127.7, 127.5, 125.7, 120.5, 83.2, 79.63, 78.5,
65.9, 56.5, 53.4, 47.2, 38.6, 36.8, 32.5, 28.4, 28.04. HRMS for
[M+H]+ Calc: 654.3137, found: 654.3138.
3. Solid phase synthesis, purification and characterization of
c-AApeptides.
The Tat 48–57 peptide P1 was synthesized and analyzed by the
USF peptide facility, and was used without further purification.
The two g-AApeptides were prepared on a Knorr resin in peptide
synthesis vessels on a Burrell Wrist-Action shaker following
the standard Fmoc chemistry of solid phase peptide synthesis
protocol. Each coupling cycle included an Fmoc deprotection
using 20% Piperidine in DMF, and 4 h coupling of 1.5 equiv of
g-AApeptide building blocks onto resin in the presence 2 equiv
of DIC (diisopropylcarbodiimide)/Oxohydroxybenzotriazole in
DMF. After the desired sequences were assembled, they were
transferred into a 4 ml vial and cleaved from solid support in
48 : 50 : 2 TFA/CH2Cl2/triisopropylsilane overnight. Then solvent
was evaporated and the residues were analyzed and purified on an
analytical (1 ml min-1) and a preparative Waters (20 ml min-1)
HPLC systems, respectively. The same methods were used by
running 5% to 100% linear gradient of solvent B (0.1% TFA in
acetonitrile) in A (0.1% TFA in water) over 40 min, followed
by 100% solvent B over 10 min. The desired fractions were
>70% in crude (as determined by HPLC) and eluted as single
peaks at > 95% purity. They were collected and lyophilized. The
molecular weights of g-AApeptides and Tat peptide were obtained
on Bruker AutoFlex MALDI-TOF mass spectrometer using a–
cyano-4-hydroxy-cinnamic acid as the matrix.
Yield was 69% in three steps. 1H NMR (400 MHz, DMSO-d6)
d (two rotamers) 7.84 (d, J = 8.0 Hz, 2H), 7.64–7.61 (dd, J =
4.0, 8.0 Hz, 2H), 7.37 (t, J = 8.0 Hz, 2H), 7.28 (t, J = 8.0 Hz,
2H), 7.14 & 6.98 (2d, J = 8.0 Hz, 1H), 6.74–6.69 (m, 1H), 4.29–
4.14 (m, 3H), 3.40–3.81 (m, 2H), 3.62–3.52 (m, 2H), 3.28–3.16
(m, 1H), 2.95–2.69 (m, 4H), 2.36–2.22 (m, 1H), 2.12–2.01 (m,
1H), 1.70–1.13 (m, 26H). 13C NMR (100 MHz, CD3OH) d (two
rotamers) 174.7, 174.4, 171.5, 171.2, 157.32, 157.3, 157.1, 143.9,
143.8, 141.23, 141.20, 127.3, 126.7, 124.7, 124.6, 119.5 78.5, 78.4,
66.1, 65.9, 53.1, 51.2, 50.1, 49.9, 49.8, 39.8, 39.5, 39.3, 31.6, 31.2,
29.7, 29.5, 29.2, 27.4, 25.2, 22.9, 22.8. HRMS for [M+H]+ Calc:
697.3807, found: 697.3796.
4. HIV-1 and BIV TAR RNA preparation26
Body-labeled RNA was prepared by in vitro transcription using
T7 RNA polymerase, a synthetic oligonucleotide template, and a
nucleotide mixture containing [R-32P]-CTP (3000 Ci/mmol). The
RNA oligonucleotides were purified by denaturing PAGE, and
concentrations were determined by UV at 260 nm. RNA was
annealed by heatingat90 ◦C and slow cooling to room temperature
in sterile H2O at a concentration of 20–100 nM. Binding assays
were performed at 4 ◦C.
5. EMSA (Electrophoretic mobility shift assay)4
g-AAPeptides or Tat 48–57 peptide and RNA were incubated in
a buffer (10 mL) containing Tris-HCl (50 mM, pH 8.0), KCl (50
mM), DTT (200 mM), tRNA (Escherichia coli) and Triton X-
100 (0.05%). The samples were fractionated by loading onto 12%
native polyacrylamide gels in 0.5% TB buffer and electrophoresed
at 15 W and 4 ◦C. Dried gels were exposed to a phosphor imaging
plate and scanned with a Molecular Dynamics phosphor imager.
Bands corresponding to free and bound RNA were quantified
using ImageQuant.
Yield was 43% in three steps. 1H NMR (400 MHz, DMSO-d6) d
(two rotamers) 11.37 (s, 1H), 10.80 (d, J = 8.0 Hz, 1H), 8.83–8.77
(m, 1H), 8.36–8.32 (m, 1H), 7.83 (d, J = 8.0 Hz, 2H), 7.64–7.59
(m, 2H), 7.38–7.34 (m, 2H), 7.30–7.25 (m, 2H), 7.20–7.16 (m, 1H),
7.04 (d, J = 8.0 Hz, 1H), 6.72 (br.s, 1H), 6.40 (br.s, 1H), 4.28–4.11
(m, 4H), 4.10–3.81 (m, 2H), 3.64–3.54 (m, 1H), 3.53–3.15 (m,
3H), 3.04–2.94 (m, 2H), 2.90 (s, 2H), 2.76–2.62 (m, 2H), 2.50–2.42
(m, 4H), 2.39 (s, 3H), 1.96 (s, 3H), 1.49–1.19 (m, 28H). 13C NMR
(100 MHz, DMSO-d6) d (two rotamers) 172.2, 171.8, 163.5, 157.9,
156.6, 152.3, 144.4, 144.25, 144.23, 144.2, 141.2, 137.7, 134.7,
Acknowledgements
This work is supported by USF start-up fund to JC and by a grant
from NIH-NIAID to GV.
6608 | Org. Biomol. Chem., 2011, 9, 6604–6609
This journal is
The Royal Society of Chemistry 2011
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