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How to pronounce benzoyl group in English?

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hey our cakes
welcome to another video so today we
will be discussing the chemical
synthesis of oligonucleotides
by the phosphorylamide method so firstly
you need to understand a few
terms what is an oligonucleotide
oligo means few so these are basically
short stretches of single stranded dna
or rna molecules what is a nucleoside
it is sugar plus nitrogenous base
nucleotide it is nucleoside
plus a phosphate finally you need to
know the nitrogenous bases
so we have adenine guanine
cytosine and thymine now one thing that
you need to
observe in all the three structures the
first three is
each of them has an exocyclic
amine group which is lacked in thymine
so thymine just has an
nh group whereas the rest of them have
an nh2 group
hold on to this piece of information you
will require it further
now this is how a typical nucleotide
looks here is the structure of
atp that is adenosine triphosphate
so we basically have the ribose sugar
the nitrogenous base and the
triphosphate
these are the building blocks of your
dna
now in our body any side reaction is
prevented
but when we do chemical synthesis these
strong nucleophiles like nitrogen oxygen
they call for some extra side reactions
so while preparing oligonucleotides
chemically
first step we need to do is we need to
block
these or add some protect protecting
group
so after doing that what we get is the
phosphoruma diet molecule
so to understand this let us see
starting
from this sugar so here in the sugar
ribose we have five carbons
starting from here so first carbon
second carbon third carbon fourth carbon
fifth carbon
as you know the first position always
contains the nitrogenous base
now in the nitrogenous base since we had
the nh2 group
we need to protect that group since
nitrogen would otherwise act as a
nucleophile
so it the protection is done by adding
this group called as the benzoyl group
so except thymine a benzoyl group is
added to
the nitrogenous bases then come down to
the third position
now this is the position where one
nucleotide
is joined to the other by a three prime
to five
prime phosphodiester bond so we need to
protect
this phosphate group as well that is
done by two groups
first one that you can see at the bottom
is
the diisopropyl amine group
so dye meaning there are two of these
similar structures and
iso is this l-shaped linkage so this is
the
iso propyl amine followed by
another group called as two sino
ethane at the five prime position
where the phosphates would attach we
have a group called as
dmt that is dimethoxy trityl
okay so at the five prime dmt
three prime diesopropylemine and
sinoethene
and to the nitrogenous bases the benzyl
group all of these together
make our phosphorumadite molecule so
this is basically the equivalent of our
atp
gtp ctbtp that we use in the body
next we have to go to who discovered
this method
so it was given by sir bruce merrifield
for which he received a nobel prize in
1984.
now what are the major steps in the
synthesis i have just outlined it
for the sake of clarity so there are
four major steps
first one is detritulation the bulky
group that i showed you
we have to remove that followed by
coupling that is joining the two
nucleotides
oxidation and capping what are the use
and what is each step we are going to
learn in detail
so firstly you have to link the
nucleotide to the column
now the method we are going to study is
called a solid phase oligonucleotide
synthesis
and why the name solid because our
nucleotides are
attached to a solid support now these
supports are of two types
cpg that is controlled pore glass or
also polystyrene
control pore glass are basically rigid
and non-swelling beads having pores
through these pores all your reagents
and nucleotides would be added
it is prefer for only nucleotides lower
than 40
because higher size oligonucleotides
would block the pores
next is polystyrene it is a highly cross
linked
structure that has good moisture and ex
moisture retaining con properties and
exclusion properties but the drawback is
you can use it only on a small scale
so this is our cpgb this is the first
nucleotide now the first nucleotide is
attached to the b
via a spacer molecule the first
nucleotide needs to be protected
using dmt or else there will be an
unwanted
reactions at this point after adding the
first nucleotide
the second step is detritulation why
because
the first nucleotide that you added to
the support needs to be
coupled to the next and for coupling we
need this side
mt so for that reason the step is
detritilation that is removal of this
dmt group
how can we do it by using tca
trichloroacetate
after tca the tmt group
is replaced by this h plus and now you
have
a ready nucleotide after
this process we need to remove any
excess tca
so we use the reagent acetonitrile
and after a wash of acetonitrile we
flush the column with
argon gas this is in order to remove any
residual acetone nitride
the third step is activation and
coupling
so once you removed your oh dmt group
and made the nucleotide free
you get this structure now to add
something
on this we need to introduce our second
nucleotide
and this right here is the
phosphoryamide molecule as you remember
we have the dmt we have two protecting
groups right here
okay so this is the second base it is
indicated by writing a base two here
now we have to activate this so that it
reacts
so for activation we use the molecule
tetrazole
what tetrazole does is it provides this
nitrogen with the h
plus since nitrogen has a lone pair it
donates it to it shares it with this
hydrogen and forms a bond
this is the activation step next
the coupling this becomes a very good
leaving group so this group right here
leaves and what we have is this o p o
m e this right here gets attached to the
hydroxy group of your first so this is
our first
nucleotide that we had attached to the
bead now this
right here would the ch2 os this
hydrogen
would react with this and you will get
this
bond that has been formed after
formation of the bond
the next step is gapping now
why do i have to cap and what are we
going to cap
so basically after doing the first step
that is
you added the first nucleotide to the
support
and you added another incoming
nucleotide but now there is a chance
that the second nucleotide or the second
base you added
didn't actually get attached to this
maybe
there are still some molecules linked on
the column
that have not undergone the activation
and coupling step
so what we need to do is the unreacted
os groups need to be capped or blocked
and that's done by treating it with
acetate
acetic anhydride so the hydrogen over
here
goes with the cs3 c double bond o
o h and forms acetic acid and what you
get
is this acetyl cap that is ch3c double
bond
o now this nucleotide will no more react
further
but you must have had the question why
do i even need to cap
it so the answer is if i don't
cap what would happen is there would be
a space that
is left so suppose let us imagine that
you had your first nucleotide right here
the first nucleotide
you added the second nucleotide now
second nucleotide
bound on this spot but was unable to
bind here it didn't bind over here
now you add the next nucleotide third
one
here it will normally stick so one two
three
but since the previous nucleotide didn't
attach to this position
this is vacant so the third nucleotide
would get added over here
now what you have done you have
basically caused a deletion mutation
unknowingly you have deleted one
nucleotide
and that is going to len cause a
disruption in the sea
in the main coding of your
oligonucleotide
and it's going to be a waste so hence we
need to cap
followed by the capping this right here
this linkage can you see
it's a tri-ester linkage which is highly
unstable because phosphorus as we know
is pentavalent
so to convert this unstable linkage into
a stable linkage
what we need to do is we need to oxidize
it
and this oxidation is carried out by
using
two reagents that is iodine and pyridine
so oxidation in presence of iodine and
pyridine
will give this structure so see this
tri ester has got converted into a
pentavalent
molecule which is now very stable
now you can keep continuing this process
to finally get
the long chain oligonucleotide so how
did we start
we linked the nucleotide to the support
after linking we need to flush it with
acetone followed by argon then
detritilation
which is done by treating it with tca
followed by again
washing with acetonitrile and then argon
activation by adding tetrazole
coupling follows the next
and then cap if any extra nucleotide
didn't bind
that is done by using acetic anhydride
and dimethyl aminopyridine oxidation
done by iodine and pyridine
and finally repeat so once you are done
making your nucleotide you need to
cleave it cause cleavage and
deprotection cleavage meaning
remove it from the support the first
nucleotide was added to the support
so that has to be removed and we have to
remove all the protecting groups
so the last molecule that you had will
still have dmt
you need to remove those now why do we
need to make all these oligonucleotides
so
first of all oligonucleotides are
required for
site-directed mutagenesis that is adding
mutations at known positions
for cloning dna sequencing
and sequencing gene libraries so it has
a wide application in biology
next what are the advantages of using
this method
it is easily automated process all the
additions are done by a machine
excess reagents are used so the reaction
is driven to completion
quite fast impurities and excess
reagents are washed away
therefore you don't need to do any
purification after each step
and it is very economical but there are
some disadvantages
that is when you want to make higher
oligonucleotides
the yield goes on decreasing so higher
the length of the nucleotide
more will be the decrease in yield
and finally it is very difficult to
monitor the efficiency
that is how efficiently each step is
carrying out how efficiently bases have
been added
that the real-time monitoring is
difficult these are my references
i hope you found this video informative
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bye

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benzoyl group::noun | Spocien Dictionary

benzoyl group

noun

/'bɛnzoʊɪl_grup/

the univalent radical derived from benzoic acid

Type	Words
Synonyms	benzoyl radical
Type of	chemical group, group, radical

How to pronounce benzoyl group in English?

benzoyl group::noun | Spocien Dictionary

abandonment

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