PAPER PRESENTATAION

ON

Bio-Encryption
SUBMITTED TO : CHAITANYA BHARATHI INSTITUTION OF TECHNOLOGY.

By
[Link] KUMAR Y.
Aakanksh
1st year ,ECE & 1st year,MECH
10881A0427 10881A0301

[Link]@[Link] Aakanksh@[Link]

From
 ABSTRACT:

Bio encryption is a new method of data storage

that converts information into DNA sequences
allows you to store the contents of an entire
computer hard-drive on a gram's worth of E. coli
bacteria...and perhaps considerably more than
that. In a presentation on their breakthrough, the
Hong Kong researchers showed how to change
the word "iGEM" into DNA-ready code. They
used the ASCII table to convert each of the
individual letters into a numerical value (i=105,
G=71, etc.), which can then be changed from
base-10 to base-4 (105=1221, 71=0113, etc.).
Finally, those numbers can be changed into their
DNA base equivalents, with 0, 1, 2, and 3
replaced with A, T, C, and G. And so iGEM
becomes ATCTATTGATTTATGT.

Principle
DNA & Basics
Bio-encryption by recombination--Principle
Nucleobases (or nucleotide bases/nitrogenous
bases/aglycones) are the parts of DNA and RNA Site-specific recombination
that may be involved in pairing. The primary systems are classified into two
nucleobases are cytosine, guanine, adenine
distinctive groups, integration-
(DNA and RNA), thymine (DNA) and uracil
(RNA), abbreviated as C, G, A, T, and U, excision and inversion systems.
respectively. Our Shufflon system use the
latter one. In this shufflon
DNA BASES – A, G, T, C
system, Rci-mediated
RNA BASES – A, G, U, C recombination occur between any repeat
sequences causing inversion of the DNA
The "skeleton" of adenine and guanine is Purine,
segments independently or in groups.
hence the name Purine-Bases. The "skeleton" of
cytosine, Uracil, and Thymine is Pyrimidine,
Rci-dependent deletion of shufflon segment
hence Pyrimidine-Bases.
flanked by the natural repeat sequences was not
occurred, i.e. , the DNA sequences between
repeat after recombination are conserved and no position, next to rci recombinase at third place.
loss of DNA sequence was found. RBS allowed ribosome binding before
translational process, so ribosome can translate
For the repeat sequence, there are mainly four the rci gene right after RBS gene. Finally, a
group.s, repeat a, b, c, d. There are seven bidirectional double terminator was allocated at
different repeat sequence in nature. There are the forth position. It allowed terminator on both
repeat 1-7. Repeat 1,2 belong to repeat a, repeat direction of transcription,
4, 6, 7 belong to repeat b, repeat 5 belongs to so there was no reverse
repeat c, and repeat 3 belongs to repeat d. transcription of rci gene
into mRNA which led to
Experiments showing that the inversion
wrong protein formation.
frequency with DNA sequences flanked by two
repeat a is the best, and it is much higher than
that with any two combination of repeat a, b, c, d
flanking the DNA sequence.

There are 12 bp sequences before every 19 bp

repeat sequence. With this sequence, it can
further enhance the inversion frequency, while
the mechanism is yet unknown. In our project,
we just need to exploit the shufflon system for
recombination. Therefore, we added the specific
12 bp sequences before every 19 bp repeat
sequence we added.

For the Rci recombinase, it is shown that the

inversion caused by the wide type (WT)  is
greater than that with modified, or point mutation
Translation is just the first step
at some positions of rci gene. Therefore, we
decide to use wide type rci recombinase in our Our system takes in a progressive approach when
project. transforming information to DNA.

 In our project, we constructed a Rci A translation table would first need to be
recombination system, with regulation of constructed by the client, the extended ASCII
expression. table with 256 characters were used as standard
in here. It is not difficult to identify DNA as a
First, a promotor, which was a lac operon, was naturally referred as a quaternary numeral
located in the beginning of the system. It allowed system, With the DNA base adenosine
users to use IPTG as a regulator to control representing the number “0”, thymine
expression of rci recombinase. The Ribosome representing “1”, cytosine representing “2” and
binding site (RBS) was allocated at second guanine representing “3”, we are essentially
encoding the 256 characters with this base-4 of the same length and secondly, homopolymer
numeral system. and repetitive regions could be reduced
significantly. This is fundamentally crucial to the
infrastructure of the DNA storage system as
homopolymer and repetitive regions in DNA
sequences are devastating to both DNA synthesis
and sequencing, with the compression algorithms
these cases would be minimal.

An infrastructure to the true, massively parallel

storage system

Incorporating a short message is not our purpose,

instead we are pursuing for a true massively
parallel storage system that one can
systematically incorporate useful information
neglecting its size.

In order to store a large piece of information such

Compression is the key
as a photograph or a dictionary, it is impossible
to include it within a single piece of DNA as this
is limited by the current DNA synthesis
technology. One approach is to fragment the
Before subjecting the DNA
information into pieces and insert them into the
sequences to synthesis, a
cells. However simply fragmenting the
compression step is subsequent to the translation
information followed by insertion to the cell
process.
would destroy all the data, as the order of these
Deflate – renowned as a lossless data fragments is unknown. To overcome such an
compression algorithm that uses a combination obstacle, a novel information system was
of Huffman coding and LZ77 algorithm, this invented. Each sequence that we are inserting
compression process is beneficial in two aspects into the bacterial cell composes of three sectors –
– firstly, more information could be included Headers, Messages and Checksum. Header is the
when comparing to the uncompressed message address of that particular message fragment,
which consist of 8 DNA bases with each 2 bases
as one unit – namely zone, region, area and multiple copies of reads could enable us to
district. The message is self-explanatory – the perform a majority voting on bases for which
message fragment itself and the checksum is an qualities are not the best. Moreover with the
identification and correction system for minor current reads assembling algorithms available –
mutations. velvet and euler for example, assembling the
reads from NGS is no longer a formidable task.

Decryption
STEP 2 : IDENTIFICATION OF REPEAT
Decryption is not simple, it consists of a three- SEQUENCES, MESSAGES AND
tier security fencing – encoding system, CHECKSUM
encryption system and checksum system, the
The second tier, with the given encryption
message could only be retrieved when enough
system – like R64 shufflon system in this case,
information is provided. Here shows the design
the repeats are known. The repeats could be
of a single data fragment:
recovered by using alignment tools such as
BLAST and the sequences in between the repeats
would be regarded as the fragment of messages,
with unknown order however. The checksum is
right behind the last repeat sequence.

The full message can be restored from data FINAL STEP : COMBINATORIAL
fragments through a series of steps: PROBLEM

The third tier, only the client would know the

STEP 1 : NEXT GENERATION HIGH-
function to derive the checksum. With the
THROUGHPUT SEQUENCING (NGS) AND
checksum formula, we are just one step before
ASSEMBLING
reaching our goal – recovering the correct
With the information-encrypted bacteria message. With different fragments of messages
provided, the plasmid DNA would be extracted provided, they are concatenated in different
and subjected to next-generation high-throughput permutations; fit the trial into the checksum
sequencing (NGS). A reason to choose high- formula, compare with that on the sequence and
throughput sequencing instead of ordinary BINGO if they are the same, or if not one would
sequencing technology would be NGS is a have to try again.
massively parallel sequencing process, which
REFERENCES:-
means there must exist multiple copies of
sequencing products (reads) that could cover a [1] [Link]
particular message stored within the DNA, these
[2][Link]