Section C
Properties of Nucleic Acids
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C1 Nucleic Acid Structure
C2 Chemical Properties of Nucleic Acids
C3 Thermal Properties of Nucleic Acids
C4 DNA Supercoiling
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
C1 Nucleic Acid Structure
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Bases
Nucleosides
Nucleotides
Phosphodiester
DNA double helix
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Bases
• Purines are bicyclic structures, include:
– Adenine and guanine
• Pyrimidines are monocyclic, include:
– Cytosine, thymine and uracil
• T or U
– The thymine base is replaced by uracil in RNA
– Thymine is 5-methyl-uracil
O
Uracil (U)
O
Thymine (T)
Section C: Properties of Nucleic Acids
NH3
Aderine (A)
NH
NH33
O
Guanine (G)
Cytosine (C)
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Nucleosides
• Nucleosides = Base+Sugar, the bases are covalently
attached to the 1'-position of a pentose sugar.
Nucleotides
5
• Nucleotides = Base + Sugar + phosphates , in the 5'position of sugar, 1 - 3 phosphates may be attached.
Phosphodiester bonds
• Covalent linkage of a phosphate group
between the 5'-hydroxyl of one ribose and the
3'-hydroxyl of the next.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
DNA double helix
• Discovery: In 1953 DNA double helix
structure were deduced by Watson
(34y) and Crick (46y)
• Structure:
– Two chains of DNA are in a righthanded double helix.
– The sugar-phosphate backbones are
on the outside, and the planar bases
in the center of the helix.
• Grooves: Between the backbone strands
run the major and minor grooves.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Base pairing
• Base pairs: The strands are joined by hydrogen bonding
between the bases on opposite strands, to form base pairs.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
C2 Chemical Properties of
Nucleic Acids
• Effect of acid
• Effect of alkali
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Effect of acid for DNA & RNA
• Complete hydrolysis
– In strong acid and at high temperatures, for example
perchloric acid (HClO4) at more than 100 C,
– nucleic acids are hydrolyzed completely to their
constituents: bases, ribose (or deoxy-ribose) and
phosphate.
• Partly hydrolysis
– In dilute acid, for example at pH 3-4, the most easily
hydrolyzed bonds are selectively broken.
– Apurinic hydrolysis: The glycosylic bonds attach the
purine bases to the ribose backbone, if they are broken the
nucleic acid becomes apurinic
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Effect of alkali for DNA
• DNA denaturation: The double-stranded
structure of the DNA breaks down; that is
the DNA becomes denatured.
Effect of alkali for RNA
• RNA hydrolysis: In alkali, the hydrolysis of RNA comes
about, because of the presence of the 2‘-OH group in
RNA, which is participated in the cleavage of the RNA
back-bone by intra-molecular attack on the
phosphodiester bond.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
C3 Thermal Properties of
Nucleic Acids
• Thermal denaturation
• Renaturation
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Thermal denaturation
• Increased temperature can cause the thermal
denaturation of DNA and RNA:
– RNA denatures gradually on heating, but
– dsDNA ‘melts’ into single strands at a defined
temperature, melting temperature (Tm),
• Tm is a function of G+C content of the DNA
• Denaturation may be detected by the change in A260.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Renaturation
• The thermal denaturation of DNA may be reversed by
cooling the solution.
• The speed of cooling has an influence on the outcome:
– Rapid cooling allows only to form dsDNA in local
regions, it is not the original dsDNA molecule.
– Slow cooling allows the sample fully double-stranded,
with the same absorbance as the original dsDNA
sample.
• The renaturation between different nucleic acid strands is
known as hybridization.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
C4 DNA Supercoiling
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Closed-circular DNA
Supercoiling
Topoisomer
Twist and writhe
Energy of supercoiling
Topoisomerases
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Closed-circular DNA
• Many DNA molecules in cells consist of closed-circular
double-stranded molecules, for example:
– bacterial plasmids;
– bacterial chromosomes;
– many viral DNA molecules.
• This means that:
– the two complementary single strands are each joined
into circles, and has no free ends;
– the molecules are twisted around one another and the
two single strands are linked together a number of turns
in the molecule.
• This turn number is known as the linking number.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Supercoiling
• Supercoiling:
– It is the helix over the helix of dsDNA;
– It happens in the closed-circular dsDNA.
• Supercoiling direction:
– Positive: the twist is in same direction as the double helix;
– Negative: the twist is in opposite direction as the helix.
• Lk and Lk
– Lk : the value for a relaxed closed circle;
– Lk: Lk = Lk - Lk, defined as the number of 360 twists
introduced before ring closure. It quantifies the level of
supercoiling.
• Example: Most natural DNA is negatively supercoiled
– DNA when isolated from cells is commonly negatively (-)
supercoiled by around 6 turns per 100 turns,
– that is Lk/Lk = -6/100 = -0.06.
Section C: Properties of Nucleic Acids
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Positive
Negative
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Topoisomer
• The Lk is a topological property of a
closed-circular DNA;
• The linking number cannot be changed
without breaking one or both of the DNA
back-bones.
• A molecule of a given linking number is
known as a topoisomer.
• Topoisomers differ from each other only
in their linking number.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Twist and writhe
• Topological changes
The conformation of the DNA can be altered while the Lk remains constant
(Fig. 2), corresponding to the types of the supercoiling (Lk), the DNA
may be:
– Completely into writhe (p45 Fig. 2a);
– Completely into twist (p45 Fig. 2c);
– Common situation is between the two extremes (2b).
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Twist and writhe
• Tw and Wr:
– Tw: Twist linking number
– Wr: Writhe linking number
• Lk = Tw + Wr:
– Lk must be an integer, but
– Tw and Wr need not.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Energy of supercoiling
• Torsional stress:
– Supercoiling can introduce torsional stress into DNA
molecules. Supercoiled DNA hence has a higher
energy than relaxed DNA.
• Roles of torsional stress:
– For negative supercoiling, this energy makes it easier
for the DNA helix to be locally untwisted.
– Negative supercoiling may facilitate the processes
which require unwinding of the helix, such as
transcription initiation or replication.
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Topoisomerases
• Topoisomerases are essential enzymes in all organisms
– Being involved in replication, recombination and
transcription.
• Topoisomerases: The enzymes that regulate the level of
supercoiling of DNA molecules are termed topoisomerases
– To alter Lk: they break transiently one or both DNA strands;
– By attacking a tyrosine residue on a backbone;
• There are two classes of topoisomerase:
– Type I: breaking one strand of the DNA, and change the Lk
in steps of ±1 (p46 Fig. 4a).
– Type II: require the hydrolysis of ATP, break both strands of
DNA and change Lk in steps of ±2 (p46 Fig. 4b).
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
Segregation
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences
That’s all for Section C
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences