Structure of DNA

Introduction

Chemical Composition of DNA

1. Nitrogenous base - either a purine or a pyrimidine
   • Purines: Adenine (A) and Guanine (G)
   • Pyrimidines: Cytosine (C) and Thymine (T)
2. Pentose sugar - 2-deoxyribose (lacks -OH at C-2 position, unlike ribose in RNA)
3. Phosphate group - links nucleotides together

Chargaff's Rules (Base Composition Rules)

• A = T (adenine always equals thymine)
• G = C (guanine always equals cytosine)
• Therefore: Purines = Pyrimidines (A + G = T + C)
• The ratio A+T / G+C varies between species (species-specific)

Watson-Crick Double Helix Model (B-DNA)

Key Features:

• DNA consists of two polynucleotide chains wound around a common central axis (helical axis) to form a right-handed double helix
• The two strands are complementary to each other

• The two strands run in opposite directions - one strand runs 5'→3' while the other runs 3'→5'
• This antiparallel arrangement is essential for replication and transcription

• The deoxyribose-phosphate backbone of each strand lies on the outside of the helix (hydrophilic, faces water)
• The nitrogenous bases face inward (hydrophobic core)
• The overall structure resembles a twisted ladder

• Adjacent nucleotides within each strand are linked by 3'-to-5' phosphodiester bonds
• A phosphoryl group connects the 3'-OH of one deoxyribose to the 5'-OH of the next
• These covalent bonds form the backbone of each strand

• Bases on opposite strands pair via hydrogen bonds (non-covalent)
• A-T pairing: Adenine pairs with Thymine - held by 2 hydrogen bonds
• G-C pairing: Guanine pairs with Cytosine - held by 3 hydrogen bonds
• A purine always pairs with a pyrimidine, so the width of the helix remains constant

• The spatial relationship of the two strands creates two grooves:
  • Major groove - wide groove; most DNA-binding proteins recognize specific sequences here
  • Minor groove - narrow groove
• These grooves allow regulatory proteins, transcription factors, and drugs to interact with DNA bases without unwinding the helix

• Hydrogen bonds between complementary base pairs
• Base stacking interactions (hydrophobic interactions between stacked bases) - actually the primary stabilizing force
• Electrostatic repulsion of phosphate groups is counteracted by metal cations (Mg2+) and histone proteins

Forms of DNA

• B-DNA is the physiologically predominant form
• Z-DNA (left-handed) may play a role in gene regulation
• A-DNA is seen under dehydrated conditions and in RNA-DNA hybrids

Strand Polarity

• A 5' end - free phosphate group at the 5' carbon of deoxyribose
• A 3' end - free hydroxyl (-OH) group at the 3' carbon of deoxyribose
• By convention, nucleotide sequences are always written 5' → 3'

Summary Table (Quick Recall)

Significance of DNA Structure

1. The antiparallel, complementary structure provides the basis for semi-conservative replication - each strand acts as a template for the new strand
2. Base pairing allows DNA to store information accurately and transmit it faithfully
3. The double helix structure provides chemical stability to the genetic material
4. The grooves serve as binding sites for proteins that regulate gene expression

Note for BPT 1st Year (Rajiv Gandhi University of Health Sciences - RGUHS): This answer covers all the standard points expected in a 10-mark long-answer question on DNA structure. For a 5-mark question, focus on: Watson-Crick model, double helix features (antiparallel, complementary base pairing, dimensions), Chargaff's rules, and significance. Always draw a diagram of the double helix showing major/minor grooves, antiparallel strands, and base pairs.