DNA Structure: The Structural Basis of Cellular Information

Chapter 16: The Structural Basis of Cellular Information

16.2 DNA Structure

Understanding the structure of DNA is fundamental to cell biology, as it underpins the mechanisms of genetic information storage, replication, and transmission. This section covers the historical discoveries, molecular features, and physical properties of DNA.

Chargaff's Rules

• Erwin Chargaff discovered that the base composition of DNA varies among species, but within a species, the percentage of adenine (A) equals thymine (T), and the percentage of guanine (G) equals cytosine (C).

• These relationships are known as Chargaff's rules and were critical in deducing the double helix structure of DNA.

• Example: If a DNA sample contains 30% A, it will also contain 30% T; similarly, if it contains 20% G, it will contain 20% C.

DNA Base Composition Data

Chargaff's rules are supported by quantitative analysis of DNA from various organisms.

Source of DNA	A (%)	T (%)	G (%)	C (%)	A+T (%)	G+C (%)	A/T	G/C
Human	30.9	29.4	19.9	19.8	60.3	39.7	1.05	1.00
Yeast	31.3	32.9	18.7	17.1	64.2	35.8	0.95	1.09
Bacteriophage T4	32.2	32.4	17.6	17.9	64.6	35.5	0.99	0.98
Additional info: Table values inferred from typical textbook data.

Watson and Crick's Double Helix Model

• James Watson and Francis Crick used wire models and existing chemical data to propose the double helix structure of DNA.

• Critical evidence came from Rosalind Franklin's X-ray diffraction images, which revealed DNA's helical nature.

• DNA consists of a sugar-phosphate backbone on the outside, with nitrogenous bases on the inside forming base pairs.

• At physiological pH, bases form hydrogen bonds with each other: A pairs with T (2 hydrogen bonds), G pairs with C (3 hydrogen bonds).

• There are 10 nucleotide pairs per complete turn of the helix, with a distance of 0.34 nm per pair and a 2-nm diameter of the helix.

• The two strands are antiparallel, meaning they run in opposite directions (5' to 3' and 3' to 5').

• The base sequence of one strand determines the complementary sequence of the other.

Key Features of DNA Structure

• DNA strands twist to form major and minor grooves, which are important for protein-DNA interactions.

• Phosphodiester bonds join the 5' carbon of one nucleotide to the 3' carbon of the next.

• Antiparallel orientation is essential for proper base pairing and replication.

Measuring DNA Length

• DNA length is measured in base pairs (bp).

• Larger stretches are measured in kilobases (kb) and megabases (Mb):

  • 1 kb = 1,000 bp

  • 10 kb = 10,000 bp

  • 1 Mb = 1,000,000 bp

Supercoiling of DNA

• The DNA double helix can be twisted upon itself to form supercoiled DNA.

• Positive supercoil: Twisting DNA further in the same direction.

• Negative supercoil: Twisting DNA in the opposite direction.

• Supercoiling occurs in both linear and circular DNA, but is more easily studied in circular DNA.

• Supercoiling helps make chromosomal DNA more compact.

Topoisomerases: Enzymes Modifying DNA Supercoiling

• Topoisomerases are enzymes that induce or relax supercoils in DNA.

• Type I topoisomerases: Introduce transient single-strand breaks.

• Type II topoisomerases: Introduce double-strand breaks; in bacteria, DNA gyrase is a type II topoisomerase.

• DNA gyrase can relax positive supercoiling and induce negative supercoiling, and is involved in DNA replication.

DNA Denaturation and Renaturation

• DNA strands are held together by weak noncovalent bonds, allowing them to be separated (denatured) by heat or pH changes.

• Denaturation increases absorbance at 260 nm; the temperature at which half the DNA is denatured is the melting temperature (Tm).

• Renaturation (reannealing) is the process by which separated strands recombine.

• Single- and double-stranded DNA differ in light absorption, allowing monitoring of these processes.

Factors Influencing DNA Melting Temperature

• GC content: G-C pairs have three hydrogen bonds, making DNA with higher GC content more stable and increasing Tm.

• Base stacking: Hydrophobic and van der Waals interactions between adjacent bases stabilize the double helix.

• Proper base pairing is essential for helix stability.

Equation:

$T_m \propto \text{GC content}$

Nucleic Acid Hybridization

• Nucleic acid hybridization is a set of techniques for identifying nucleic acids based on sequence complementarity.

• Leads to the formation of DNA-DNA, DNA-RNA, or RNA-RNA hybrids.

• Denatured DNA is incubated with a probe (purified single-stranded DNA) complementary to the target sequence.

• Used in fluorescence in situ hybridization (FISH) to visualize specific DNA sequences in cells.

• Example: FISH can be used to detect chromosomal abnormalities or gene locations.

Summary Table: Key Terms and Definitions

Term	Definition
Chargaff's Rules	A = T, G = C in DNA; base composition varies among species
Double Helix	Two antiparallel strands of DNA twisted into a helical structure
Supercoiling	Additional twisting of the DNA helix upon itself
Topoisomerase	Enzyme that alters DNA supercoiling by breaking and rejoining strands
Denaturation	Separation of DNA strands by heat or pH
Renaturation	Recombination of separated DNA strands
Base Pair	Pair of complementary nucleotides (A-T, G-C) in DNA
Antiparallel	Opposite orientation of the two DNA strands
FISH	Fluorescence in situ hybridization; technique for visualizing DNA sequences

Additional info: Some table values and explanations were inferred from standard cell biology textbooks to ensure completeness and clarity.