DNA Structure and Base Pairing

DNA Structure

• Double-stranded DNA has two antiparallel strands that are complementary.
• Base pairing rules: A always pairs with T (2 hydrogen bonds), and G always pairs with C (3 hydrogen bonds).
• As a result, the amount of A equals the amount of T, and the amount of G equals the amount of C.
• Total purines (A and G) equal total pyrimidines (T and C), known as Chargaff's rules.

DNA Conformation

• Most DNA occurs as a right-handed double-helical molecule known as Watson-Crick DNA or B-DNA.
• The hydrophilic sugar-phosphate backbone of each strand is on the outside of the double helix.
• Hydrogen-bonded base pairs are stacked in the center of the molecule, with about 10 base pairs per complete turn of the helix.
• A rare left-handed double-helical form of DNA, known as Z-DNA, occurs in G-C–rich sequences.

DNA Function and Interaction

• Antitumor drugs like daunorubicin and doxorubicin intercalate between DNA bases, interfering with topoisomerase II and preventing proper DNA replication.
• Other drugs, such as cisplatin, bind tightly to DNA, causing structural distortion and malfunction.

Topoisomerases and Supercoiling

• Topoisomerases are enzymes that can change the amount of supercoiling in DNA molecules by making transient breaks in DNA strands.
• For example, DNA gyrase (DNA topoisomerase II) can introduce negative supercoiling into DNA.

Nucleosomes and Chromatin

• Nuclear DNA in eukaryotes is found in chromatin associated with histones and non-histone proteins.
• The basic packaging unit of chromatin is the nucleosome, where DNA is wound around a histone octamer.
• Histone H1 is associated with linker DNA between nucleosomes, helping to package them into a solenoid-like structure.
• Further condensation occurs to form the chromosome.

Chromatin Structure

• Euchromatin corresponds to loosely associated nucleosomes (10-nm fibers).
• Heterochromatin is more highly condensed, producing interphase heterochromatin and chromatin characteristic of mitotic chromosomes.

Denaturation and Renaturation of DNA

• Double-helical DNA can be denatured by conditions that disrupt hydrogen bonding and base stacking, resulting in the "melting" of the double helix.
• Denatured single-stranded DNA can be renatured (annealed) if the denaturing condition is slowly removed.
• Renaturation is an important step in probing a Southern blot and in performing the polymerase chain reaction.

Organization of DNA

• Large DNA molecules must be packaged to fit inside the cell and still be functional.
• Mitochondrial DNA and the DNA of most prokaryotes are closed circular structures that can exist as relaxed circles or as supercoiled structures.
• Supercoiling results from strain on the molecule caused by under- or overwinding the double helix.