tRNA on Ribosome

tRNA on Ribosome and how to wrap in and stop antigens with nucleic acids
    Around traffic light - Click image to download.          Helsenotis        
New drug  – a chance
 
I found these articles supporting my theory about amino acids` binding to their cognate codons (triplets):
Idea in biochemistry part 1-4:


PART 1

Quick web searches on the topic ribosome all show the same:
the amino acid-loaded tRNA arrives at the ribosome with its
anti-codon first. I think this could be an oversimplification, which
doesn`t take notice to the probable, intuitive fact that the gene is
a blueprint for the protein, a mirror-copy made through evolution.
Say the proteins initially instructed the genes and not vice versa.
Say the food came first, and then the means to carry it.

For such a complex process as translation to proceed without many errors,
there has to be another, more primary mechanism of proofreading. Maybe there is a
closer link between amino acids and the mRNA than previously thought.

Maybe there is a transient key-lock binding between the amino acid and
the codon before the anticodon binds.
The bases, adenine (A), guanine (G), uracil (U), thymine (T), and cytosine (C) seems to reach for the amino acids, and the first and the second
bases seem to play the greatest role. For instance, the short one-cyclic U are
in the second (midst) position in codons binding hydrophobic amino acids,
indicating the hydrophobic aa`s R-groups (side chains) will turn downwards/inwards (towards the codons, away from the water) when binding.
And hydrophilic amino acids have the longer two-cyclic A in the midst position
in their respective codons, indicating the R-groups will turn upwards/outwards, away from the codons,
towards the water when encountering the codons.

My point is that it should be possible to make any short gene sequence
that could match any protein, almost as an antibody. The oligonucleotides
will be shrunk at point of binding, and they will probably work for only shorter 
stretches. As far as I know it should not be too dangerous to apply in vivo,
but of course animal tests, research etc. are needed. 
I read for instance in Discover Magazine and at Nature.com that eosinophilic cells 
catapult mitochondrial DNA nets against parasites (malaria).

It should be possible to target any protein-markers in any disease,
and hence destroy the culprits. Say, put a virus in a PCR machine and make
cheap copies of tailored antibodies! Or use the new oligo synthesis factories!

I try to explain my theory in this video:
http://www.youtube.com/watch?v=7834CXASQF8 

I found these articles supporting my theory about amino acids` binding to their cognate codons:

http://www.ncbi.nlm.nih.gov/pubmed/14561881?dopt=Abstract’,’NCBI’,’700′,’400′)

Sincerely,

Ottar Stensvold,

Reinhold Zieglers veg 14 B

6414 Molde
Norway
mobile: +47 95 177 433
epost: ottarstensvold@hotmail.com

web: http://ottarstensvold.spaces.live.com

born:  February 7th 1971
——————————————

PART 2

A drop of ordinary water-smear on a microscopy slide reveals a pattern:
the bacteria in the water lines up, symbolized like this:  o…..o..o…o…o
These lines are best seen at 400x magnification. See example picture at bottom of this page.
My theory / idea is that DNA from ruptured bacteria binds and absorbs proteins
from its own species.
So what? If so, if a nucleic acid can bind to a protein in a coded manner,
then the aptamer technology is the tech of the future.
Say for instance the codon GUG, which codes for the amino acid valine, weakly
binds this amino acid. Symbolized like this: E-<
The codon-amino acid binding gives several combinatorial possibilities with
regard to polar interactions, mechanic fit and R-group placement.
If we can make aptamers tailored to bind specific proteins, then we can
take down any pathogen.
—-
PART 3
 
The amino acid sequence of the HIV surface protein GP 120
can be found at GenBank:

http://www.ncbi.nlm.nih.gov/protein/7769644?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum

My plan is to try to make an array of different aptamers to hit this protein.
The approach I will use is basically to design aptamers that are based on
the amino acids` corresponding codons. In the DNA-aptamers, I will replace
U with T, and in the third wobble-position I will choose the assumed least
interfering base (e.g. T, i.e. Thymine). RNA aptamers can also be used.
There is a chance that the aptamers will match directly.
The matches have to be at accessible parts of the protein`s surface.
The aptamers will be ordered (outsourced), for instance from:

http://www.biomers.net/upload/Image/Preislisten/DNA_En_EUR.pdf


or from Eurogentec in San Diego, California:

http://www.eurogentec.com/news/106-eurogentec-launches-new-oligo-synthesis-facility.html

 
The price of the aptamers will be maybe around one tenth of comparable drugs,
i.e. monoclonal antibodies.

The stock of different aptamers will be annotated at my portable computer.

Then, step 2, we have to beg institutions which store HIV viruses to test the aptamers in vitro.
The results can be viewed with electron microscopes.

(One can also test aptamers on oncoproteins in stored tissue samples,
e.g. the 17 aa-sequence in the CD44 protein which is over-expressed on membranes on glioma cancer brain cells.)

This project needs help from media. The headlines could be:

“Burn off money to test HIV drug”
“Find needle in haystack”

Press: “Will this be tested in humans? Will there be marketing? Sales?
Investing?”

Answer:  “We will find a balanced solution, it`s fair that developed
countries pay for some of the venture.”

The task will require all communication skills and business intelligence.

It is a bit like cloud computing: once the hidden codes are found,
they have to be administered.

It is my goal to reach this goal of my life!

—————————————— 

 
PART 4
 
The aptamer:

GGTTGGTGTGGTTGG
(or ggttggtgtggttgg)

 
or GGT TGG  TGT   GGT  TGG
or GGU UGG UGU GGU UGG  (in RNA) corresponds to the amino acids:
gly     trp    cys     gly   trp   abbreviations:
G      W        C      G      W

This aptamer bind to the blood coagulation factor protein thrombin.
I found it at:
http://bloodjournal.hematologylibrary.org/cgi/content/abstract/83/3/677?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=aptamer&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT

To find the amino acid sequence in thrombin,  I search GenBank at:
http://www.ncbi.nlm.nih.gov/nuccore/169808403?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum

The combination “GW” occurred once in the thrombin protein,
the combination “WG” occurred twice,
the combination “WC” occurred twice,
the combination “GC” occurred twice,
and the combination “CG” occurred three times.

The latter combination, for instance, should then bind to the aptamer-codons UGU GGU.

I did not find similar matches in the comparable plasma proteins albumin or insulin,
and I think further research will find no other similar matches either.
It is striking that the aptamer comprises the range of codons encoding the protein (aa range) it binds!
 
The numbers of possibilities to get a twosome aa-combination of a pool of twenty different amino acids,
should plainly speaking be 1/20*1/20 = 1/400,
and this makes specific binding likely!
 
This underscores my suggestion that proteins can bind specific to their codon combinations in mRNA or sense (+)ssDNA.
In the June 2009 Scientific American issue, there is an article about silent mutations (by Chamary and Hurst)
which highlights that different codons encoding the same amino acids give alterations in the proteins.
It`s thus feasible that this bias is caused by the codons` positioning of the amino acids (R-group placement in space). Such a moulding will give a hand-glove fit which can be harnessed in aptamer-drug design.

For pictures of bacteria in water, see this site: http://iceberg.dri.edu/blogs4.php

 

Sincerely,

Ottar Stensvold

Molde

Norway

(Regarding autoimmune MS and diabetes:
My idea is to take down the protein markers
which the T-cells home in on when they perform autoimmunity, and/or target the receptors /
surface proteins on the T-cells which they use in this task. At GenBank we can find some of
the needed gene/protein sequences.)

I try to explain my theory in this video:
http://www.youtube.com/watch?v=7834CXASQF8

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About ottarstensvold

Molde Norway
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5 Responses to tRNA on Ribosome

  1. For clarity, the elongation factor binding to and shepherding aminoacyl-tRNA is omitted in the model.

  2. Pieces of genetic material can survive digestion and reach blood-circulation through oral supplementation: http://www.newscientist.com/article/mg21128323.100-eating-your-greens-alters-your-genes.html

  3. Archemix (www.archemix.com ) is leading the development of aptamers as a new class of directed therapeutics for the prevention and treatment of chronic and acute diseases. ARC1779, its lead proprietary candidate, is a potent, selective, first-in-class antagonist of von Willebrand Factor (vWF).
    (Wikipedia)
    – Interestingly, this aptamer constitutes several three-codons matching translationally corresponding three-amino acids in the large vWF protein, giving a theoretical specific binding affinity of 1/8000!

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