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Understanding DNA and RNA Structure: A Comprehensive Guide

Explore the intricate world of DNA and RNA structure through nucleotides, nucleosides, and higher-order RNA structures. Learn about the chemical forces holding DNA strands together and different ways of depicting DNA structure. Discover the significance of base composition in DNA melting curves and its role in molecular biology techniques.

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Understanding DNA and RNA Structure: A Comprehensive Guide

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  1. DNA & RNA Structure Fig 1.9

  2. Deoxyribonucleic acid (DNA) • is the genetic material • Stores genetic information in the form of a code: a linear sequence of nucleotides. • Replicated by copying the strands using each as a template for the production of the complementary strand.

  3. 3 Ways of Depicting DNA Structure

  4. Nucleosides (of DNA) – Precursors to Nucleotides Nucleoside = base + sugar Sugar = deoxyribose; 5 carbons, no OH on the 2nd (or 2’) carbon; base is attached to carbon 1

  5. The 4 Nucleotides (precursors) of DNA γβα

  6. RNA Ribose replaces deoxyribose; uracil replaces thymine

  7. e.g., AMP is a ribonucleotide, dAMP is a deoxyribonucleotide

  8. In DNA and RNA, nucleotides are held together by phosphodiester bonds.

  9. Higher Order RNA Structure Stem-loops are common elements of secondary RNA structure. Stems are double-stranded regions of RNA that are A-form helices. They usually follow Watson-Crick base pairing rules (U replaces T), but other pairs occur (G – U is common). (DNA is typically a B-form helix). Stem loop

  10. Secondary structure diagram Tertiary structure diagram Tetrahymena rRNA intron Cr.LSU rRNA intron

  11. What chemical forces hold (or drive) the DNA strands together? (also applies to double-stranded regions of RNA)

  12. 1. Hydrogen bonds between bases Also important that the purine-pyrimidine base pairs are of similar size.

  13. 2. DNA strands also held together by base stacking: Van der Waals interactions between successive (or neighbor) base-pairs Evidence: Compounds that interfere with Hydrogen bonds (urea, formamide) don’t separate strands by themselves, still requires heat 3. Double-stranded helix structure also promoted by having phosphates on outside, interact with H2O and counter ions (K+, Mg2+, etc.)

  14. Double-stranded (DS) DNA statistics (B-form) • Helix is right handed • 10 base-pairs/turn • 3.4 nm (34 angstroms)/turn • Helix has a major groove and a minor groove.

  15. 3 Ways of Depicting DNA Structure

  16. 10 1 0

  17. Molecular Visualization:www.umass.edu/microbio/chime/ DNA Structure: www.umass.edu/molvis/tutorials/dna/

  18. Study Helix Stability with Melting Curves DNA melting curve of Streptococcus DNA. When DNA melts, the 2 strands come apart, and its absorbance in the UV region increases. Tm= temp. at which 50% of DNA is melted.

  19. Re-Annealing or Hybridization Works with: • DNA - DNA • DNA - RNA • RNA - RNA Basis of many techniques in molecular biology.

  20. Base composition (G-C content) determines melting temperature: varies among organisms

  21. G-C content also determines density of DNA (g/cc) Separation of nuclear (nuc) and mitochondrial (mt) DNA on a CsCl-ethidium bromide gradient – visualized with long-wave UV light.

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