1. Section C Properties of Nucleic Acids
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

2. C1 Nucleic Acid Structure
Bases
Nucleosides
Nucleotides
Phosphodiester
DNA double helix
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

3. 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
Aderine (A)
Guanine (G)
Thymine (T)
NH3 O
Uracil (U)
Cytosine (C)
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

4. Nucleosides Nucleotides Phosphodiester bonds
Nucleosides = Base+Sugar, the bases are covalently attached to the 1'-position of a pentose sugar. 5
Nucleotides
Nucleotides = Base + Sugar + phosphates , in the 5'-position of sugar, 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

5. 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 right-handed 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

6. 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

7. C2 Chemical Properties of Nucleic Acids
Effect of acid
Effect of alkali
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

8. 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

9. 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

10. C3 Thermal Properties of Nucleic Acids
Thermal denaturation
Renaturation
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

11. 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

12. 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

13. C4 DNA Supercoiling Closed-circular DNA Supercoiling Topoisomer
Twist and writhe
Energy of supercoiling
Topoisomerases
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

14. 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

15. Supercoiling Supercoiling: Supercoiling direction: Lk and Lk
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 =
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

16. Positive Negative Yang Xu, College of Life Sciences
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

17. 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

18. 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

19. 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

20. 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

21. 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

22. Yang Xu, College of Life Sciences
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

23. Segregation Yang Xu, College of Life Sciences
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences

24. That’s all for Section C
Section C: Properties of Nucleic Acids
Yang Xu, College of Life Sciences