Lecture 1 Flashcards
what are the forces that influence nucleic acid structure (DNA and RNA)
base stacking, base pairing, ionic interactions
what determines whether DNA lies on the single or double stranded sides of the eq?
the delta G of the reaction-
what has a greater delta G for base stacking?
GC bonds
where does base stacking occur
double stranded DNA molecules
what is the greatest contributor to the stability of a DNA double helix
base stacking; bases stacked on top of each other attract each other through transient dipole-dipole interactions.
T or F: base stacking is sequence dependent
true; GC/GC is not the same as CG/CG
why it is more beneficial for bases to pair with each other rather than H bonding with water molecules?
due to cooperativity that comes from having hydrogen bonds between the same two molecules
how do cations contribute to the ionic interactions that help stabilize DNA helices
they shield repulsion between the negatively charged phosphates in the backbone. the cations are separated from the phosphates by water molecules
what does. me
does native conformation DNA or denatured have a higher absorbance?
denatured DNA has a higher absorbance than native dna
what factors affect DNA stability
- length of DNA strands (increases)
- the amount of mismatches (lowers)
- high GC = higher MT
- organic solvents = hlower MT
- salts increase mT
- extremem pH means less stable
properties of B dna
- Right handed
- 10 bp/turn
- width: 2.4 nm
- pitch length (length of a turn): 3.4 nm
- base pair spacing: 0.34 nm
- has a slight base tilt and a propeller twist
- major and minor groove
how does the nature of the solvent contribute to the DNA stability
- ethanol is less polar than water; therefore, in ethanol DNA favours a double helix because there might
A-DNA
- right handed
- 11 bp/turn
- great base tilt
- found in rna double helices/RNA-dna type structures
- has a very exaggerated major and minor groove
Z-DNA
- alternating pU-pY
- Left handed due to that alternating pattern
- 12 bp/turn
