DNA Structure

Lecture Date: 9/17/25

Chargaff

  • worked on purifying DNA from different molecules

  • DNA is composed of nucleotides

  • Took DNA from different organisms and digested them into the four different nucleotides and then compared the ratios of the different nucleotides present

  • Counted up how many of each nucleotides are in each DNA

  • Found that there were specific ratios ins which for every Adenine there was a Thymine and for every Guanine there was a Cytosine

  • This tells us how the nucleotides on either strand of the DNA bind to one another (A binds to T, C binds to G)

Chargaff’s Rules

  1. The base composition of DNA varies from one species to another

  2. Different tissues of the same organism have the same base composition

  3. The base composition of DNA in a given species does not change with an organism over time

  4. In all cellular DNA the number of adenosine residues is equal to the number of thymidine residues and the number of guanosine redisdues is equal to the number of cytosine residues

Purines vs. Pyrimidines

  • Trick: the shorter word (Purine) corresponds to the larger (double ring structure)

  • Purines contain a six carbon ring and a five carbon ring

  • Pyrimidines contain only a six carbon ring

  • Chargaff describes the binding in DNA between the nitrogenous bases

Pauling

  • Suggested a structure of DNA that was incorrect

  • Proposed that DNA was a triple helix

  • This is wrong because the bases do not pair with one another which does not support chargaffs rule and he had the phosphate groups on the inside of the DNA structure which is incorrect because phosphate groups are negatively charged so they would want to be on the exterior because the similar charges cause repulsion and greater repulsion can occur when the phosphate groups are on the exterior and are not confined to a small space

X-ray Crystallography

  • A method used to determine the arrangement of electrons which can be used to figure out where other atoms are present

  • Roseline Frankin

  • This method was needed for Watson and Crick’s research

Hydrogen Bonding

  • A and T are joined by two hydrogen bonds

  • G and C are joined by three hydrogen bonds

  • Since G and C have more hydrogen bonds they are stronger bonds which can influence the structure of DNA

Major vs. Minor Groove

  • Major Groove: Has more exposed nitrogenous bases which causes this area to have a higher chance of bonding to other molecules

  • Minor Groove: fewer exposed nitrogenous bases which means that fewer proteins will bind to this area

Watson and Crick Summary

  • DNA is a double helix

  • Anti-parallel

  • Hydrogen bonded base pairs on the inside

  • Sugar-Phosphate backbone on the outside

  • Each chain runs 5’ to 3’

  • DNA is negatively charged because of the phosphate groups that have a negative charge

  • Model hints at how DNA works

Dickerson Dodecamer

  • Created a molecule of a known sequence that was 12 units long and then analyzed the structure using X-ray crystallography

  • Results of this differed from the Watson and Crick helix in minor ways

  • Used a segment that was complementary to itself so that he did not need to synthesize two strands of DNA

  • Found that the 3D structure of DNA varies with the sequence of DNA

  • This did not contradict Watson and Crick because it instead suggested that the details can differ from the general structure when observed on a smaller scale in terms of the number of nucleotides present

Drawing DNA Structure For Exam:

  • Know how to draw the structure of each base as well as how they are oriented in the structure (see below)