11.2 DNA structure and organization

DNA structure and organization are fundamental to understanding genetic information. This topic explores the double helix, base pairing, and various helical forms. It also covers how DNA is packaged in cells, from nucleosomes to higher-order chromatin structures.

The physical properties of DNA, including supercoiling, denaturation, and renaturation, are crucial for its function. These concepts lay the groundwork for understanding DNA replication, transcription, and other processes involving nucleic acids.

DNA Structure

Helical Structure and Base Pairing

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• DNA molecule consists of two antiparallel polynucleotide strands that wind around each other to form a right-handed double helix
• Strands are held together by hydrogen bonds between complementary base pairs following Watson-Crick base pairing rules
  • Adenine (A) pairs with thymine (T) via two hydrogen bonds
  • Guanine (G) pairs with cytosine (C) via three hydrogen bonds
• Sugar-phosphate backbones of the two strands are on the outside of the double helix, while the bases are stacked inside
• Diameter of the double helix is approximately 20 Å (2 nm)

Grooves and Helical Forms

• Double helix has two types of grooves: major groove and minor groove
  • Major groove is wider and deeper, allowing proteins to interact with the bases more easily
  • Minor groove is narrower and shallower
• Different helical forms of DNA exist depending on environmental conditions and sequence composition
  • A-DNA is a right-handed double helix with a shorter, wider structure compared to B-DNA (found in dehydrated samples)
  • B-DNA is the most common form under physiological conditions, with 10.5 base pairs per helical turn
  • Z-DNA is a left-handed double helix that forms in regions with alternating purine-pyrimidine sequences (GC repeats)

DNA Packaging

Nucleosomes and Chromatin

• In eukaryotic cells, DNA is packaged into chromatin to fit within the nucleus
• Basic unit of chromatin is the nucleosome, which consists of:
  • Histone octamer core (two copies each of histones H2A, H2B, H3, and H4)
  • 147 base pairs of DNA wrapped around the histone octamer (~1.7 turns)
• Linker DNA connects adjacent nucleosomes and is associated with histone H1
• Nucleosomes are arranged like "beads on a string" to form the 10 nm chromatin fiber
• Higher-order packaging of chromatin involves further compaction into the 30 nm fiber and higher-order structures

Supercoiling

• DNA can undergo supercoiling, a process that introduces additional twists or writhes into the double helix
• Positive supercoiling (overwinding) occurs when the double helix is twisted in the direction of the helix, increasing the number of turns
• Negative supercoiling (underwinding) occurs when the double helix is twisted in the opposite direction, decreasing the number of turns
• Supercoiling plays a crucial role in DNA packaging and can influence processes such as replication and transcription
• Topoisomerases are enzymes that regulate the level of supercoiling by introducing or removing supercoils

DNA Properties

Denaturation and Renaturation

• DNA denaturation is the process by which the double helix unwinds and separates into single strands
  • Caused by factors such as high temperature, extreme pH, or chemical denaturants (urea, formamide)
  • Hydrogen bonds between base pairs are disrupted, but the sugar-phosphate backbone remains intact
• Renaturation (reannealing) is the process by which single-stranded DNA molecules reassociate to form a double helix
  • Occurs when denaturing conditions are removed and complementary strands find each other
  • Rate of renaturation depends on factors such as DNA concentration, sequence complexity, and ionic strength
• Melting temperature (Tm) is the temperature at which 50% of the DNA is denatured
  • Depends on factors such as GC content (higher GC content leads to higher Tm) and salt concentration