Physical Properties of nucleic acids

• Nucleic acids


  DNA and RNA, exhibit a variety of physical properties that arise from their molecular structure and interactions
• Polynucleotide structure


  • Nucleic acids are composed of long chains of nucleotides
  • Each nucleotide consists of a phosphate group, a sugar molecule and a nitrogenous base
  • The sequence of these nucleotides determines the genetic information encoded in the molecule
• Double helix structure


  • DNA forms a double helix, where two polynucleotide chains wind around each other in a twisted ladder-like structure
  • This helical structure is stabilized by hydrogen bonds between complementary base pairs, as well as hydrophobic interactions between stacked base pairs
• Flexibility


  • Despite their rigidity as individual base pairs, nucleic acid chains are flexible, allowing them to adopt various conformations
  • This flexibility is important for processes such as DNA replication, transcription, and protein binding
• Melting temperature (Tm)


  • The temperature at which half of the DNA strands in a double helix are dissociated into single strands
  • Tm is influenced by factors such as the length and sequence of the DNA, the concentration of ions, and the presence of certain chemical modifications or ligands
• Absorbance spectra


  • Nucleic acids absorb ultraviolet (UV) light at wavelengths around 260 nanometers (nm) due to the presence of aromatic rings in their nitrogenous bases
  • This property is often used to quantify and characterize nucleic acids in laboratory experiments
• Electrophoretic mobility


  • Nucleic acids are negatively charged molecules due to the phosphate groups in their backbone
  • Consequently, they migrate towards the anode (positive electrode) in an electric field during gel electrophoresis, with the rate of migration influenced by factors such as size, shape, and conformation
• Complex formation


  • Nucleic acids can form complexes with various molecules, including proteins, small molecules, and metal ions
  • These interactions play crucial roles in processes such as gene regulation, DNA repair, and chromatin structure
• DNA denaturation


  • The ability of the double helix DNA to separate the two strands
  • When a DNA solution is heated enough, the hydrogen bonds that hold the two strands together weaken and finally break (DNA melting)
• DNA renaturation


  When the temperature of a DNA solution is low enough, the hydrogen bonds form again, and finally, all hydrogen bonds are restored
• Melting temperature (Tm)


  The midpoint of the temperature range over which the DNA strands are half-denatured
• Slipped structures


  • Usually occur at tandem repeats and are usually found upstream of regulatory sequences in vitro
  • During replication, the DNA sequences are associated, and the DNA polymerase can recognize and bind to the 3' end of the DNA strand, allowing it to synthesize an identical complementary copy
• Cruciform structures


  • Paired stem-loop formations that can be found in vitro for many inverted repeats in plasmids and bacteriophages
• Triple helix DNA


  • A third strand of DNA joins the first two to form triplex DNA
  • Triple helix DNA occurs at purine-pyrimidine stretches in DNA and is favored by sequences containing a mirror repeat symmetry
• Tertiary structure of DNA

  • The higher-order organization of the double helix into complex three-dimensional shapes
  • Includes supercoiling, bending and looping, protein-DNA complexes, and higher-order structures
• Handedness


  • Asymmetrical molecules with the same parts and connectivity can be identical, or they can be mirror images of each other. Some molecules are "right-handed" while others are "left-handed" mirror images of these
• Length of helix turn

  • The angle of bonds between nucleotides causes most nucleic acids to form a helix shape. But small differences in the shape of the helix can cause differences in how the helix interacts with our enzymes and other molecules
• Number of base pairs per turn

  • This can be chemically and biologically important, as it determines which enzymes and molecules can affect the DNA or RNA
• Difference in size between major and minor grooves

  • In a nucleic acid double helix, the "major groove" is the wider path that opens between the two nucleic acid strands. The "minor groove" is the narrower one
• Gene expression


  • The process by which the information stored in DNA is used to synthesize functional molecules, such as proteins or RNA molecules
  • It involves transcription and translation
• DNA replication


  • The process by which a cell duplicates its DNA prior to cell division
  • During replication, the double-stranded DNA molecule unwinds and separates into two strands, each of which serves as a template for the synthesis of a new complementary strand
• DNA repair


  • Cells are constantly exposed to various sources of DNA damage, and DNA repair mechanisms detect and correct these damages to maintain the integrity of the genome
  • Several pathways exist for repairing different types of DNA damage
• Regulation of gene expression


  • Cells tightly regulate the expression of their genes to adapt to changing environmental conditions and developmental cues
  • This regulation occurs at multiple levels, including transcriptional, post-transcriptional, and epigenetic
• RNA processing


  • RNA molecules undergo various processing steps to generate mature, functional RNAs
  • For example, in eukaryotic cells, pre-mRNA molecules undergo splicing to remove introns and join exons, producing a mature mRNA that can be translated into protein
• DNA repair mechanisms


  • Detect and correct damages to maintain the integrity of the genome
• Pathways for repairing different types of DNA damage

  • Base excision repair
  • Nucleotide excision repair
  • Mismatch repair
• Regulation of Gene Expression


  Cells tightly regulate the expression of their genes to adapt to changing environmental conditions and developmental cues
• Levels of gene expression regulation

  • Transcriptional regulation (e.g., through transcription factors and enhancer elements)
  • Post-transcriptional regulation (e.g., through microRNAs and RNA-binding proteins)
  • Epigenetic modifications (e.g., DNA methylation and histone modifications)
• RNA Processing


  RNA molecules undergo various processing steps to generate mature, functional RNAs
• RNA processing in eukaryotic cells

  1. Pre-mRNA molecules undergo splicing to remove introns and join exons, producing a mature mRNA

  2. RNA molecules may undergo modifications such as methylation and editing to fine-tune their stability and function
• RNA-mediated Processes


  RNA molecules participate in a diverse array of cellular processes beyond their role as intermediates in gene expression
• Examples of RNA-mediated processes


  • Ribosomal RNA (rRNA) and transfer RNA (tRNA) are essential components of the protein synthesis machinery
  • Small regulatory RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), play key roles in gene regulation and defense against viruses
• Chromatin Structure and Organization

  • DNA is packaged in the cell nucleus as chromatin, a complex of DNA, histone proteins, and other associated proteins
  • Chromatin structure is dynamically regulated to control access to the underlying DNA sequence, influencing processes such as transcription, DNA replication, and DNA repair
• Dysregulation of these nucleic acid-based cellular activities can lead to various diseases, including cancer, neurodegenerative disorders, and developmental abnormalities
• DNA Replication


  • The process by which a cell makes an identical copy of its DNA prior to cell division
  • Essential for the faithful transmission of genetic information to daughter cells
  • Occurs in multiple stages and involves several key enzymes and proteins
• DNA Replication Initiation


  1. DNA replication begins at specific sites along the DNA molecule called origins of replication

  2. Initiator proteins bind to the origin and recruit other proteins necessary for the initiation of replication
• DNA Replication Unwinding


  Enzymes called helicases unwind the DNA by breaking the hydrogen bonds between the complementary base pairs, creating a replication fork where the two strands separate
• Primer Synthesis


  Primase synthesizes RNA primers complementary to the DNA template, providing a free 3'-OH group for DNA polymerases to add nucleotides
• DNA Synthesis


  1. DNA polymerases catalyze the addition of nucleotides to the growing DNA strand

  2. The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously in the opposite direction, producing Okazaki fragments
• Proofreading and Correction


  DNA polymerases have proofreading activity, allowing them to detect and correct errors that may occur during DNA synthesis