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whetzel at stanford.edu
Wed May 19 21:51:11 PDT 2010
Interesting. I too am having problems with the text you sent, but the
text below works fine (text from the first element for nanoparticle on
the resource page). I can report this as a bug. Do you have a
comment on the priority for this?
Montet et al. reported a detailed synthesis of cRGD-CLIO(Cy5.5) (5).
Initially, a linear RGD peptide GSSK(FI)GGGCRGDC (IRGD) was obtained
with the Fmoc method as a C-terminal amide and oxidized via bubbling
air to yield a disulfide-linked cRGD peptide in 0.1 M ammonium
bicarbonate. The amino-CLIO nanoparticle was synthesized in several
steps. The starting material, monocrystalline iron oxide (MION), was
synthesized by neutralization of ferrous salts, ferric salts, and
dextran with ammonium hydroxide, followed by ultra-filtration (14).
The obtained MION was cross-linked in strong base with epichlorohydrin
and then reacted with ammonia to produce amino-CLIO (CLIO-NH2) (14).
Finally, CLIO-NH2 was reacted with the N-hydroxysuccinimide ester of
Cy5.5 (Amersham Biosciences Corp., Piscataway, NJ), followed by
peptide attachment using disuccinimidyl suberimidate to produce cRGD-
CLIO(Cy5.5) (5). There were ~250 amines, 8,000 iron atoms, 27
peptides, and 8 Cy5.5 molecules per CLIO-NH2 nanoparticle.
On May 19, 2010, at 9:37 PM, Nigam Shah wrote:
> The synthesis of FITC-BCDDDGQRLGNQWAVGHLM-CLIO-Cy5.5 (BN-CLIO-CY5.5)
> and FITC-BCDDDGQMLGNHLAVGQWR (ScrBN-CLIO-Cy5.5, control peptide) was
> described by Montet et al. (1). In brief, the peptides were
> synthesized using solid-phase peptide synthesis via 9-
> fluorenylmethyloxycarbonyl (Fmoc) chemistry. The N-terminus beta-
> alanine (B) was used to conjugate with FITC and the thiol group of
> cysteine was utilized to conjugate the peptide with CLIO-Cy5.5
> nanoparticles. CLIO-NH2 nanoparticles (produced by coating iron
> oxide nanoparticles with dextran, followed by cross-linking with
> epichlorohydrin, and then activated by reacting with ammonia (13,
> 14)) were mixed with Cy5.5 solution to produce 5.1 dyes per
> nanoparticle. Purified CLIO(NH2)-Cy5.5 was further activated by
> reacting with succinimidyl iodoacetate. Activated CLIO-Cy5.5 was
> then conjugated with a BN peptide through cysteine. The size of the
> nanoparticle was determined to be 35 nm using laser light scattering
> method, with an average of 50 peptides per iron oxide particle.
> .. is the exact text.
> On Wed, May 19, 2010 at 9:36 PM, Nigam Shah <nigam at stanford.edu>
> Anything .. I just took the second element from MICAD that shows up
> on the "nanoparticle" resource page.
> On Wed, May 19, 2010 at 9:19 PM, Trish Whetzel
> <whetzel at stanford.edu> wrote:
> Hi Nigam,
> Can you send the input text?
> On May 19, 2010, at 8:31 PM, admin at bioontology.org wrote:
> Name : Nigam Shah
> Email : nigam at stanford.edu
> Annotator is non responsive as of 8:30 PM, pacific time on
> 5/18/2010. Small amount of text, with just one ontology to annotate
> with (NPO) .. takes over 5 minutes and no response comes back.
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
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