Download Palindromic Sequences

Welcome to
Molecular Biology Through Discovery
Tuesday, 18 September 2012
DNA Structure / Sanger & Tuppy
General Questions
What would you like discussed in class,
on any subject that has already come up?
The mentor list
and clarification on who,
what,
when,
etc.
Who can we pick,
how many can we choose from?
What are we turning in exactly on Thursday???
DNA Structure
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
#1: Hello!
#2: Complete description
of our civilization
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
...
TAGGCCACTGCCCAACCCTCCAT
CATAAAACTTGGGCTTGGGAGG
CAGAGCCTAACCTCTCTCACTCT
AGACAGGTCTAAGATGATTGGG
AACGAAATGAGCCGTCTCGACTT
TTTCGCGAAGTGGCTAA ...
DNA Structure
Biology Today
and Tomorrow
Starr, Evers, and
Starr (2010)
DNA Structure
Biology:
Understanding
Life
Alters (2000)
DNA Structure
E. How can the helical structure of DNA and
internucleotide distance be discerned from
Franklin and Gosling's x-ray photograph?
DNA Structure
E. How can the helical structure of DNA and
internucleotide distance be discerned from
Franklin and Gosling's x-ray photograph?
DNA Structure
It's necessary to be slightly
underemployed if you are
to do something significant.
- Jim Watson
O
NH
N
N
P
NH
N
N
N
-O
O
2
N
O
O
N
O
O
O
-O
O
P
O
From the nucleotides shown above,
construct a double-stranded DNA
fragment with the sequence ACTG.
You may:
duplicate (Ctrl-d)
horizontal flip (Alt-hgoh)
vertical flip (Alt-hgov)
and/or rotate (Alt-hgor)
the nucleotides, but you may not
change the relative positions of
their atoms.
N
NH
NH
N
O
2
O
-O
P
N
N
O
O
O
-O
O
P
O
NH
2
DNA Directionality & Palindromes
SQ10. If one strand of DNA had
the sequence 5'-GGACT-3',
what would be the sequence
of the second strand?
DNA Directionality & Palindromes
I understand what a
palindrome is in English
but when it comes to DNA
how come 5'-AGTTGA-3'
isn't a palindrome when
it's anti-parallel strand is
3'-TCAACT-5' which is also
a palindrome.
Palindromic Sequences
What is it?
Backwards = forwards
ROTATOR
What about with DNA?
GCTATCG
• DNA is double stranded
TTAATGTGAGTTAGCTCACTCATT
AATTACACTCAATCGAGTGAGTAA
Palindromic Sequences
What is it?
Backwards = forwards
ROTATOR
What about with DNA?
GCTATCG
• DNA is double stranded
• DNA is redundant
TTAATGTGAGTTAGCTCACTCATT
AATTACACTCAATCGAGTGAGTAA
Palindromic Sequences
What is it?
Backwards = forwards
ROTATOR
What about with DNA?
GCTATCG
• DNA is double stranded
• DNA is redundant
• DNA has direction (read 5’->3’)
5’- TTAATGTGAGTTAGCTCACTCATT -3’
3’- AATTACACTCAATCGAGTGAGTAA -5’
AATGAGTGAGCTAACTCACATTAA
Palindromic Sequences
5’- TTAATGTGAGTTAGCTCACTCATT -3’
3’- AATTACACTCAATCGAGTGAGTAA -5’
TA
T G
GC
AT
GC
TA
GC
TTAAT TCATT
AATTA AGTAA
CG
TA
CG
DNA: cruciform
AT
CG
RNA: stem/loop
G T
AT
Palindromic Sequences
5’- TTAATGTGAGTTAGCTCACTCATT -3’
3’- AATTACACTCAATCGAGTGAGTAA -5’
UA
U G
GC
AU
GC
UA
GC
UUAAU UCAUU
DNA: cruciform
RNA: stem/loop
tRNA
Palindromic Sequences
why [are] palindromes…
targeted by DNA-binding proteins
why palindromes are targeted by DNA-binding proteins
Palindromic Sequences
NNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTNNNNNNNNNNNNN
NNNNNNNNNNNNNN
NNNNNNNNNNNNN
AATGAGTGAGCTAACTCACATTAA
recognizes GTGAGTT
Palindromic Sequences
NNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATTNNNNNNNNNNNNN
NNNNNNNNNNNNNN
NNNNNNNNNNNNN
AATGAGTGAGCTAACTCACATTAA
recognizes GTGAGTT
Palindromes: Serve as binding sites for dimeric protein
gene
5’-GTA
3’-CAT
GTA
..(8)..
TAC
..(8)..
..(8)..
TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN
ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
gene
5’-GTA
3’-CAT
GTA
..(8)..
..(8)..
TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN
ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
Transcription
RNA
factor
RNA Polymerase
..(8)..
TAC
Is the promoter a beginning
string of nucleotides for RNA,
Sanger and Tuppy (1951)
Phe-Val-Asp-Glu-His-Leu-Cys-Gly
Thr-Pro-Lys-Ala
Gly-Glu-Arg-Gly-Tyr-Leu-Val-Cys-Gly
Ser-His-Leu-Val-Glu-Ala
Sanger and Tuppy (1951)
Sanger and Tuppy (1951)
Insulin is a dimer, composed of one A chain (fraction A) and a B chain
(fraction B). Sanger and Tuppy determined this experimentally by oxidizing
insulin with performic acid. The sequence of fraction B was determined
experimentally as being at least composed of phenylalanine, valine, aspartic
acid, and glutamic acid, and well as threonine, proline, lysine, and alanine.
This was done using a prepared sample of polypeptide fragments, which were
separated through a process known as paper chromatography. A similar
process was done for fraction A. From all the studies perform, the overall
structure and cross linking between chains can be deduced. Cross-linking can
occur on cysteine residues, because they contain sulfur atoms, capable of
dimerizing with one another and forming stable covalent bonds. Overall, two
phenylalanine and two glcyl chains were determined to be the subunits of this
particular form of insulin.
Sanger and Tuppy (1951)
Now, how this was deduced was through a number of
chromatography tests where different chemicals were used in
order to split insulin at different bond points and then examine
the fragments. In the first section we can see
Phe.Val.Asp.Glu.His.Leu.CySO3H.Gly which has been
determined by the following: B4β2, B1α2, B2γ8, B1α1, B1β8,
B1γ1, B1α6, B1β13, B1γ4, B1β10, B1α5, B1γ7, B1β12, B4β1,
B1γ6, B1β5. Where B1α1 refers to the test number and type,
then spot number.
Sanger and Tuppy (1951)
1. Cys-Gly
B1a.1
Sanger and Tuppy (1951)
1. Cys-Gly
B1a.1
Sanger and Tuppy (1951)
1. Cys-Gly
2. Leu-Cys
B1a.1
B1a.6
Sanger and Tuppy (1951)
1. Cys-Gly
B1a.1
2. Leu-Cys
B1a.6
3. Leu-Cys-Gly #1 & #2
Sanger and Tuppy (1951)
Sanger and Tuppy (1951)
1. Cys-Gly
B1a.1
2. Leu-Cys
B1a.6
3. Leu-Cys-Gly #1 & #2
Results vs Conclusions
Kaleigh
Jonathan
Michael
Colleen
Bobby
Supriya
Tayab
Abdul
Cailin
Sue
Kristen
Shahroze
Mandi
Shaun
Abdallah
Celeste
Neda
Yordanos
Me
And go to CyanoBIKE
Sanger and Tuppy (1951)
Coming Attractions
Benzer (1959)
Goodbye from
Molecular Biology Through Discovery
Tuesday, 18 September 2012
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
ACTG
G-O-O-D-B-Y-E
ACTG
ACTG
ACTG
ACTG
ACTG
...