Week 2 - Structure and Properties of Nucleic Acids Flashcards
A-form adaptations
- dsRNA
- dehydrated crystals
Z-form adaptations
- dsDNA
- dehydrated crystals
Z-form DNA in cells
proved through immunofluorescence during germination
evidence for function in Z-form DNA
- purine/pyrimidine tracts
- dynamic observation of Z-form DNA in cells with immunofluorescence
- proteins that specifically bind to DNA
poxvirus
protein forms complex with Z-DNA
vaccination
cow pox was injected to form immunization against poxvirus
cruciform structures
- depends on palindromes and self-complementarity
- formed when palindromic sequences are exposed too much during replication and transcription (DNA unwinds in these processes)
staggered palindrome
- a gap in palindromic structures
- more common
overlapping palindrome
- no gap in palindromic structures
- less common
hairpin bends
staggered palindromic sequences that enables formation of cruciform structure
negative consequences of cruciform structures
- leads to an extra chromosome, leading to Trisomy syndrome (bits of 11 and 22 incorporated)
- rate of swapping is proportional to length of palindrome
- longer palindrome results in a larger chance to form cruciform
three-stranded structures in nucleic acids
- requires extra hydrogen bond (non-WC bonds)
- triple helix
- H-form DNA
Hoogsten pairs
non Watson and Crick pairs
triple helix
- 3 nucleic acid molecules
- third strand runs parallel instead
mirror repeat
- reflection on a single strand.
- most do not have a gap
H-DNA
- only in ds DNA
- folding back must be a mirror sequence
- homopyrimidine and homopurine sequences favour the formation of H-form DNA
H-DNA biological role
- does it occur in the cell? not sure
- distribution of homopurine:homopyrimidine sequence in genome? statistical over-representation in genome; found at specific locations
- are there H-form DNA binding proteins? some proteins have been found to bind these special regions
quadruple helix
steric hindrance
bulge
a single nucleotide with nothing to pair with
internal loop
region that loops out because it is not base paired
hairpin bends
single stranded (4-6) nucleotide with 180 degree turn to form intrastrand double helix
complex secondary structures of RNA molecules
single strand parts will stack up to 3D shape
factors that affect the folding of secondary structure of nucleic acids
- changes in pH
- changes in temp
- addition of polar substances
- changes in salt concentration
melting temperature of DNA in relation to GC content
- proportional relationship
- CG bp makes 3 H-bonds
- CG base stacking interactions are greater
AT base pairs
regions rich in AT base pairs denature most readily
hybridization
- annealing/rewinding of double stranded helix between complementary nucleic acids (DNA and RNA)
- spontaneous, therefore occurs under favourable, non denaturing conditions (lower temperature, high salt concentration, no extreme pH)
ideal conditions in a hybridization experiment
- dependent on the % complementarity to look for
- example: if the melting temp is 72 degrees and 75% complementarity is desired, temperature should be lower
electrophoresis
- nucleic acids contain a net negative charge therefore they will migrate in an electric field.
- conducted in agarose or acrylamide gel
speed of nucleic acids
- proportional to voltage
- proportional to charge on molecule
- inversely proportional to MW
- inversely proportional to friction/length
- speed = E x q/length x MW
intercalating fluorescent dyes
complex, aromatic organic molecules that intercalate in between bases due to hydrophobic effect
unresolved zone
too clustered and too long as they have no run long enough
resolution zone
- can be used for analysis as it had run long enough
- distance migrated is proportional to length of bp
overresolved zone
have run for too long and is not visible for analysis
using lines to determine fragment length
line of best fit must go through data point or it will introduce error
