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
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
13.
14.
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.
20.
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
22.
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..
25.
26.
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
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