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Title: DNA structure and topology
Description: This notes contains informative notes regarding structure of DNA,their arrangements etc.
Description: This notes contains informative notes regarding structure of DNA,their arrangements etc.
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STRUCTURE OF THE DOUBLE HELIX
• THREE MAJOR FORMS
– B-DNA
– A-DNA
– Z-DNA
B-DNA
• B-DNA IS BIOLOGICALLY THE MOST COMMON
– RIGHT-HANDED (20 ANGSTROM (A) DIAMETER)
– COMPLEMENTARY BASE-PAIRING (WATSON-CRICK)
• A-T
• G-C
– EACH BASE PAIR HAS ~ THE SAME WIDTH
B, A and Z forms of DNA
B-DNA
• IDEAL B-DNA HAS 10 BASE PAIRS PER TURN
• BASE THICKNESS
– AROMATIC RINGS WITH 3
...
4 = 34 A PER COMPLETE TURN
AXIS PASSES THROUGH MIDDLE OF EACH BP
MINOR GROOVE IS NARROW
MAJOR GROOVE IS WIDE
A-DNA
•
•
•
•
•
RIGHT-HANDED HELIX
WIDER AND FLATTER THAN B-DNA
11
...
"Nicked Open-Circular" DNA has one strand cut
...
"Linear" DNA has free ends, either because both strands have been cut, or
because the DNA was linear in vivo
...
"Relaxed Circular" DNA is fully intact with both strands uncut, but has been
enzymatically "relaxed" (supercoils removed)
...
"Supercoiled Denatured" DNA is like supercoiled DNA, but has unpaired
regions that make it slightly less compact; this can result from excessive
alkalinity during plasmid preparation
...
* "Supercoiled" (or "Covalently Closed-Circular") DNA is fully intact with
both strands uncut, and with a twist built in, resulting in a compact form
...
Negative supercoils: the DNA is twisted about its axis in the direction
opposite to the intrinsic winding of the helix, thus releasing the torsional
pressure or unwinding the helix
...
The linking number (L): the number of times that the two strands of the
double helix of a closed molecule cross each other in total
...
Different Topological Domains
a) Circular DNA
b) Chromosomal DNA loops
c) Linear DNA attached to membrane
d) Linear DNA attached to protein aggregates
DNA Topology
• “SUPERCOILING” : DNA’S “TERTIARY STRUCTURE
• L = “LINKING NUMBER”
– A TOPOLOGIC INVARIANT
– THE # OF TIMES ONE DNA STRAND WINDS AROUND THE OTHER
• L = T + W
– T IS THE “TWIST
• THE # OF COMPLETE REVOLUTIONS THAT ONE DNA STRAND MAKES
AROUND THE DUPLEX AXIS
– W IS THE “WRITHE”
• THE # OF TIMES THE DUPLEX AXIS TURNS AROUND THE
SUPERHELICAL AXIS
Hypothetical circular DNA molecule in
which DNA strands are linked once
TOPOLOGICAL STATES OF COVALENTLY CLOSED CIRCULAR DNA
DNA Topology
• THE TOPOLOGICAL PROPERTIES OF DNA HELP US
TO EXPLAIN
– DNA COMPACTING IN THE NUCLEUS
– UNWINDING OF DNA AT THE REPLICATION FORK
– FORMATION AND MAINTENANCE OF THE TRANSCRIPTION
BUBBLE
• MANAGING THE SUPERCOILING IN THE ADVANCING
TRANSCRIPTION BUBBLE
Two Forms of Writhes
Interwound /
Plectonemic Writhe
Toroidal / Spiral Writhe
Processes that can have adverse effects on DNA superstructure:
1) the double-helical structure of DNA contorts and supercoils when
unwound by polymerases or helicases
...
Failure to resolve these problems can promote misregulation of
gene expression and chromosomal breakage, and can have severe
consequences for cell viability
Title: DNA structure and topology
Description: This notes contains informative notes regarding structure of DNA,their arrangements etc.
Description: This notes contains informative notes regarding structure of DNA,their arrangements etc.