3.1 DNA structure and properties

DNA, the blueprint of life, is a complex molecule with a fascinating structure. Its double helix shape, made of nucleotides, allows for efficient storage and replication of genetic information. Understanding DNA's composition is crucial for grasping how it functions in living organisms.

Base pairing rules and chemical properties give DNA its unique abilities. These features enable DNA to store, transmit, and replicate genetic information with high fidelity. Exploring DNA's structure and properties helps us comprehend its role in fundamental biological processes.

DNA Composition and Structure

Nucleotide Components and Organization

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• DNA (deoxyribonucleic acid) forms a polymer composed of nucleotide monomers
• Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base
• Four nitrogenous bases in DNA include adenine (A), guanine (G), cytosine (C), and thymine (T)
  • A and G classified as purines
  • C and T classified as pyrimidines
• Sugar-phosphate backbone forms the exterior of the double helix
• Nitrogenous bases orient towards the interior of the double helix
• DNA typically exists as a double-stranded molecule
  • Two strands run antiparallel to each other (5' to 3' in opposite directions)

DNA Structure Dimensions

• DNA double helix diameter measures approximately 2 nanometers
• Each complete turn of the helix contains about 10.5 base pairs
• One complete turn measures 3.4 nanometers in length
• These dimensions allow for efficient packing of genetic material within the cell nucleus
• Structural properties facilitate interactions with proteins involved in DNA replication, transcription, and repair

Base Pairing Rules in DNA

Chargaff's Rules and Base Pair Ratios

• Chargaff's rules dictate the base pair ratios in DNA
• Amount of adenine equals thymine (A=T)
• Amount of guanine equals cytosine (G=C)
• Maintains a 1:1 ratio of purines to pyrimidines
• These ratios crucial for maintaining DNA structure and stability
• Chargaff's observations provided key insights leading to the discovery of DNA's double helix structure

Watson-Crick Base Pairing

• Watson-Crick base pairing defines specific nucleotide interactions
• Adenine pairs with thymine via two hydrogen bonds (A-T)
• Guanine pairs with cytosine via three hydrogen bonds (G-C)
• Specificity of base pairing ensures fidelity of genetic information storage and transmission
• Base pairing rules critical during DNA replication and transcription processes
• Stronger G-C base pairing contributes to increased stability in DNA regions with higher GC content
  • Affects processes such as DNA melting and PCR (Polymerase Chain Reaction)

Applications of Base Pairing Rules

• Complementary nature of DNA strands enables various molecular biology techniques
• DNA sequencing relies on base pairing for accurate determination of nucleotide order
• Hybridization techniques (Southern blotting, microarrays) utilize base pairing for specific DNA detection
• PCR amplification depends on base pairing for primer annealing and template replication
• CRISPR-Cas9 gene editing exploits base pairing rules for precise targeting of DNA sequences

Properties of DNA

Chemical Stability and Interactions

• DNA exhibits remarkable chemical stability due to its sugar-phosphate backbone
• Protection of bases within the double helix structure enhances overall stability
• Negatively charged phosphate groups contribute to DNA's hydrophilic nature
• Hydrophilic properties allow DNA to interact with proteins and other molecules in the cellular environment
• DNA's stability enables long-term storage of genetic information across generations

Denaturation and Renaturation

• DNA undergoes denaturation (melting) in response to changes in temperature or pH
• Denaturation separates the two strands of the double helix
• Renaturation (annealing) occurs when conditions return to normal, reforming the double helix
• These processes important for many molecular biology techniques (PCR, DNA sequencing)
• Melting temperature (Tm) of DNA depends on factors such as GC content and salt concentration

Replication and Information Storage

• Antiparallel nature of DNA strands enables semiconservative replication
• Each daughter molecule contains one parental strand and one newly synthesized strand
• High fidelity of genetic information storage and transmission due to stable structure
• Proofreading mechanisms during replication further ensure accuracy of genetic information
• DNA's ability to store and replicate genetic information fundamental to life processes

DNA Conformations: A-DNA vs B-DNA vs Z-DNA

B-DNA: The Most Common Form

• B-DNA represents the most common form found under physiological conditions
• Characterized by a right-handed helix with 10.5 base pairs per turn
• Features a wide major groove and narrow minor groove
• Major groove provides easy access for protein interactions (transcription factors)
• Minor groove interacts with specific DNA-binding proteins and small molecules

A-DNA and Z-DNA Structures

• A-DNA forms a right-handed helix with 11 base pairs per turn
• A-DNA occurs under dehydrating conditions or in RNA-DNA hybrids
• A-DNA exhibits a narrower and deeper major groove compared to B-DNA
• Z-DNA forms a left-handed helix with 12 base pairs per turn
• Z-DNA typically occurs in alternating purine-pyrimidine sequences
• Z-DNA plays a role in certain regulatory processes (transcription, recombination)

Factors Influencing DNA Conformations

• Transitions between DNA conformations influenced by various factors
• Hydration levels affect the formation of A-DNA vs B-DNA
• Salt concentration impacts DNA conformation and stability
• Presence of specific proteins or small molecules can induce conformational changes
• Different DNA conformations affect accessibility of bases to proteins and other molecules
• Understanding DNA conformations crucial for structural biology experiments (X-ray crystallography, NMR spectroscopy)