Algorithm to find G-Quadruplex in a DNA sequence

1.  HIRA BATOOL
 MAIRA KHAN
 MARYAM ZAHRAH
 NADIA ASHRAF

3. NEXT
GENERATION
SEQUENCING

4.  Determining the sequence of the nucleotides i.e. A,T,C,G
along a DNA strand
 Why DNA to be sequenced…???
 To know the order of nucleotides which will enable us to:
› To know about genes
› Find information about the architecture of the genome
› Comparative genome analysis

5.  Plus-minus strand sequencing
 Maxam-Gilbert chemical sequencing
 Sanger`s chain termination sequencing (Dye
termination sequencing)
 The most used method for last 30 years!

6.  By the passage of time new techniques were
developed which replaced old techniques
because they were:
› Old
› Time consuming
› Laborious
› Expensive
› Hazardous(used hazardous reagents)
› Volume of reagents and space

7.  Roche’s (454) GS FLX Genome Analyzer

8.  Illuminas Solexa 1G sequencer

9.  Applied Biosystem’s SOLiD system

10.  Helicos

12.  A DNA sequence that initially binds the RNA
polymerase.
 Upstream to the transcription start site.
 Core promoter refers to the minimal set of
sequence elements required for accurate
transcription Initiation.
 Usually -35 to +35

15.  - 37 TO -32
 Consensus sequence: G/C G/C G/A CGCCC
 Recognized by TFIIB.
 The TFIIB–BRE interaction facilitates the
assembly of a TFIIB–TBP–TATA complex

16.  -31 to – 26
 Consensus sequence : T A T A A/T A A/T
 Recognized by TBP( a subunit of TFIID)
 In Humans, 32% of 1031 potential promoter
regions have one.
 Primary role is formation of pre-initiation
complex(promoters + General TF).

17.  -2 TO +4
 C/T C/T A+1 N T/A C/T C/T
 Recognized by TFIID
 Nucleates PIC formation in TATA less
promoter
 facilitates the binding of Transcription
Factor II D (TBP)..

18.  + 28 to +32
 A/G G A/T CGTG
 Recognized by TFIID
 DPE plays a major role at TATA-less
promoters.

19.  +18 TO +29
 Consensus sequence: CSARSSAACGC
 cooperate with the initiator to stimulate
transcription.
 NO TATA in these promoters.

21.  DNA sequences in which Four guanine bases
can associate through Hoogsteen hydrogen
bonding to form a square planar structure
called a G-tetrad, and two or more G- tetrads
can stack on top of each other to form a G-
quadruplex.
 Repeats of at least 3 guanine residues are
separated by loops of 1-7 other base pairs

23.  Present in DNA, RNA, LNA (locked), PNA
(peptide)
 Across a wide range of species, G4 DNA motifs
were found in telomeres, G-rich micro- and
mini-satellites, near promoters, and within the
ribosomal DNA (rDNA)

24.  Important components of human telomeres,
and play a role in regulation of transcription
and translation.
 They are also interesting as nanotechnological
devices..

27.  Generally, a simple pattern match is used for
searching for possible quadruplex forming
sequences:
 G3+N1-7G3+N1-7G3+N1-7G3+
where N is any base (including G)
.

28.  Text = Promoter or Telomere sequence
 Pattern= GGG
 N=text.length( )
 M=pattern.length( )
 Count=0 [ count the no of G’s]
 Array[i][j] [ stores start and end position]
 i=0 [stores start]
 For(t=0;t<=N;) [scans Text]
{
for(p=0;p<=M;) [scans Pattern]
{
if(text[t]==Pattern[p])
{
p++;
t++;
count++;
}
else
t++; count=0

29. if(count>=M)
{
j=0;
array[i][j]=t -2; [stores start]
array[i][j+1]=t; [stores end]
i++;
}
t= prefix function( )
if(arr[i][j] – arr[i-1][j+1] >0 && arr[i][j]- arr[i-
1][j+1]!<=7)
{
t= prefix function( )
}
}
}

31.  http://www.ploscompbiol.org/article/info%3
Adoi%2F10.1371%2Fjournal.pcbi.1000861
 http://www.ncbi.nlm.nih.gov/pmc/articles/P
MC1636468/
 Quadruplex.org

32.  R Purine (A or G)
 Y Pyrimidine (C or T)
 N Any nucleotide
 W Weak (A or T)
 S Strong (G or C)
 M Amino (A or C)
 K Keto (G or T)
 B Not A (G or C or T)
 H Not G (A or C or T)
 D Not C (A or G or T)
 V Not T (A or G or C)

33.  PNA's backbone is composed of repeating N-
(2-aminoethyl)-glycine units linked by peptide
bonds. The bases are linked to the backbone
by methylene carbonyl bonds.
 LNA The ribose moiety of an LNA nucleotide is
modified with an extra bridge connecting the
2' oxygen and 4' carbon