Structural Organization and Chemical Properties of DNA

Strand Orientation and Structural Framework

• DNA consists of two strands that run in opposite directions, a property described as being antiparallel.
• Each strand of DNA is a polymer constructed of deoxyribose sugars.
• Every sugar molecule within a strand is attached to a base that juts out toward the opposing strand.
• In double-stranded DNA, the two strands are typically coiled around each other in the spatial arrangement of a double helix.

Base Pairing Complementarity and Hydrogen Bonding

• Each base in each strand is paired directly with another base across from it on the opposite strand:
  • Base G on one strand pairs specifically with base C on the opposing strand.
  • Base A on one strand pairs specifically with base T on the opposing strand.
• Proper base pairing is maintained by weak hydrogen bonds formed between opposing bases:
  • There are $3$ hydrogen bonds in the case of base G paired with base C.
  • There are $2$ hydrogen bonds in the case of base A paired with base T.
• The accumulation of these hydrogen bonds helps to hold the two paired strands together.

Hydrophobic Interactions and Base Stacking Forces

• The bases themselves are inherently hydrophobic.
• Water molecules in the surrounding medium tend to keep the bases aggregated together in a stack.
• The stacked bases also experience weak Van der Waals attractions, which further assist in stabilizing the overall base stacking interaction.