Molecular Basics: DNA structure
DNA just is. And we dance to its music.
Richard Dawkins (1995), p. 133.
DNA is often perceived as simply a very long sequence of base
pairs. DNA can twist, buckle, roll, tilt, stretch, shear, rise, slide,
and shift!
Dr. Mohammed Qaisiya
DNA – The Twentieth Century’s
Greatest Scientific Discovery
The four major players _Francis Crick, Maurice Wilkins, James Watson, and Rosalind Franklin
_(Clockwise from top left)_in the discovery of the double-helix structure of DNA.
X-Ray Diffraction
• Is a technique used to provide information about the structure of
the molecule as well as the organization of it’s components.
• The atomic and molecular structure of the molecule is
determined after crystallization process to form a crystal, in
which crystalline atoms cause the beam of X-ray to diffract into
many directions and by measuring the angles and intensities of
the diffracted beam the three dimensional shape will be
determined.
Chargaff’s Rule 1928
• A few years before Watson and Crick proposed the three-dimensional structure of
DNA, Erwin Chargaff developed a paper chromatography method to analyze the
amount of each base present in DNA.
• Chargaff observed certain regular relationships among the molar concentrations
of the different bases .
• These relationships are now called Chargaff ’s rules. He showed that the number
of A residues in all DNA samples was equal to the number of T residues; i.e. [A] =
[T], where the molar concentration of the base is denoted by the symbol for the
base enclosed in square brackets. Accordingly, the number of G residues equals
that of C: [G] = [C]. Finally, the amount of the purine bases equals that of the
pyrimidine bases: [A] + [G] = [T] +[C].
• RNA (Ribonucleic Acid)
• DNA (Deoxyribonucleic Acid)
Primary structure: the components of nucleic
acids
• Five-carbon sugars
• Ribose sugar OR deoxyribose ribose
• The five carbon atoms in each pentose sugar
are assigned numbers 1ʹ through 5ʹ (clockwise after O atom)
• The phosphate functional group
• Nitrogenous bases
Nucleosides and Nucleotides
• A DNA or RNA chain is formed in three steps:
• Each base is chemically linked to one molecule of sugar at
the 1ʹ-carbon of the sugar, forming a compound called a
nucleoside.
• When a phosphate group is also attached to the 5ʹ-carbon
of the same sugar, the nucleoside becomes a nucleotide.
• Nucleotides are joined (polymerized) by condensation
reactions to form a chain
Formation of nucleic acid chains
Nomenclature of nucleotides
The primary structure of DNA
Understanding this
directionality (polarity) is
critical for understanding
aspects of replication and
transcription
DNA sequence is written
with the 5 ʹ end to the left,
and the 3 ʹ end to the
right. This is also the
direction of synthesis
sugar + phosphate =
Backbone
The Length of DNA and RNA
The number of base for RNA. Number of base pairs (bp) for DNA
kb or kbp = 1000bp. Mb or Mbp = 1,000,000
microRNA (miRNA) is a small non-coding RNA molecule (containing
about 22 nucleotides)
Oligonucleotides: short chains of single-stranded DNA (usually less
than 50 bases)
Probe: is a fragment of DNA or RNA of variable length (less than
1000 bases long) which can be labeled
Primer: is a short strand of RNA or DNA (generally about 18-22
bases) that serves as a starting point for DNA synthesis
The Secondary structure of DNA
Various chemical forces drive the formation of the DNA double helix. These
include hydrogen bonds “Watson–Crick” or “complementary” base pairing,
between the bases and base stacking by hydrophobic interactions.
The Secondary structure of DNA
Various chemical forces drive the formation of the DNA double helix. These
include hydrophobic interaction “core” driving force to from helix structure.
relatively flat bases tend to stack on top of one another by means of a helical
twist = Base stacking feature
The Secondary structure of DNA
❑Hydrogen bonding could
only occur if the polarity of
the two strands ran in
opposite directions. dsDNA
is antiparallel
(5 ʹ → 3 ʹ and 3 ʹ → 5 ʹ ).
❑ The two bonds that attach a
base pair to its deoxyribose
sugar rings are not directly
opposite.
❑ The sugar–phosphate backbone
is not equally spaced
This result in major and minor groove
Alternative double-helix structures
DNA can undergo reversible strand separation/hybradization
DNA can undergo reversible strand separation/hybradization
Depend on GC content
DNA can undergo reversible strand separation/hybradization
Unusual DNA structures
DNA has heterogeneity and flexibility in form
Dynamic change in secondary and tertiary structures
Unusual structures are generally sequence specific
A- Slipped structures
“tandem repeat” : DNA is two or more adjacent, approximate copies
of a pattern of nucleotides, arranged in a
head to tail fashion 5 ʹ -TACGTACGTACGTACG- 3 ʹ
Function
1. Are found upstream of regulatory sequence
2. Target for enzymes that cut phosphodiester bonds in single-stranded DNA
3. importance for DNA–protein interactions
4. Expansion in repeat may cause neurological disorders
Friedreich’s ataxia and triple helix DNA
H.W: Huntington’s disease: XXX repeat ?
Unusual DNA structures
B- Cruciform structures
Inverted repeats are base sequences of identical composition on the complementary
strands.
They read exactly the same from 5 ʹ → 3 ʹ on each strand (in other
words, the sequence reads the same from left to right as from right
to left) = Palindromes
Function: regulatory elements in DNA replication and gene expression
Unusual structures
C- Triple Helix
- A third strand of DNA joins the first two to form triplex DNA.
-Favored by sequences containing a mirror repeat symmetry
- Occur through Hoogsteen hydrogen bonds pairing
The Tertiary structure of DNA
Underwinding (negative supercoiling makes it easier to open)
replication origins and gene promoters
Supercoiling:
reduced activity in replication and transcription
Important for chromosome condensation in bacteria
DNA molecules of almost all organisms exhibit Negative Supercoiling (Why).
Topoisomerase enzyme relax supercoiled DNA
DNA that have the same sequence yet differ in their linkage
number are referred to as topological isomers (topoisomers)
Topoisomerases: are highly conserved enzymes that convert one
topoisomer of DNA to another by changing the Linking number