Nucleic Acid Structure Flashcards
What are the forces that influence nucleic acid structure?
base stacking, base pairing, ionic interactions
applies to DNA and RNA
Which force influences DNA stability the most?
base stacking
base pairing HB is important for structure but less in stability
base stacking depends on…
sequence-dependent
order matters: AT vs TA on top
What is base stacking?
induced dipole and partial charge interactions between rings of bases (nitrogen atoms)
PI BOND STACKING
∆G of stacking is
the stability of base stacking; equilibrium of free energy btwn ss vs ds
more -ve = more stable
Which bases affect ∆G of stacking more?
G’s and C’s make more -ve = more stable
-> when G is on top of C
GC*GC -> -2.17
why is base stacking sequence dependent?
different charge and hydrophobic interactions result
hydrophobic groups together and opposite partial charges together
ss nucleic acid has higher ∆G because
no base stacking bc no base pairing
-> HB present with water
What is the advantage of ds to ss in HB?
ds = HB between bases
ss = HB between base and H2O
ds advantage = cooperativity
What are ionic interactions?
cations shield repulsion between negative phosphates
what are cation-DNA interactions mediated by?
H2O
What are the better cation shielding agents?
divalent (Mg2+) over monovalent (Na+, K+)
What does a DNA melting curve show?
increase in absorbance as temperature increases
higher GC content -> higher melting temperature
What are the 5 factors that influence DNA stability?
- length and sequence of DNA strands
- degree of complementarity
- nature of solvent
- [] and types of ions present
- pH
equation for melting temperature?
Tm = 2(A+T) + 4(G+C)
what is the effect of complementarity on DNA stability?
mismatches have steric effects -> pur-pur = lose helix and base stacking
What is intra-base pair coordinates?
movement of bases; degree of freedom between HB bases
What are the types of intra-base pair coordinates?
- shear
- buckle
- stretch
- propeller
- stagger
- opening
what are inter-base pair (step) coordinates?
base stacking that gives DNA flexibility to interact w/ other proteins
Why does DNA form a double helix?
- hydrophobic structures are driven together so that they aren’t exposed to water
- phosphate sugar backbone can’t form structures where bases are directly ontop of each other
What are the dimensions of a base pair?
20Å - base pair to base pair
3.4Å = 0.32nm - height of base pair
2.6Å - space between base pairs on top
6.0Å - middle of bp to middle of next bp
Why is the space between base pairs on top of each other 2.6Å?
space is large enough for water to fit through
bases are pushed together because…
water forms ordered networks around the hydrophobic regions -> unfavourable entropy
minimize water - hydrophobic interaction
Why must there be a space between base pairs on top of each other?
steric hinderence of phosphate backbones due to inflexibility
why can’t we have stair-like structure of DNA?
side by side or front and back
a lot of exposed hydrophobic bases area
this is why we need a TWIST -> helix
what is the pitch length?
length of 1 complete turn of B-DNA
3.4 nm
average or ideal B-DNA double helix is
10 bp/turn
right-handed
lowest energy conformation
what is the width of B-DNA? what does it include?
~2 nm/20Å
from phosphate to phosphate
if you look down a helix…
it is a perfect cylinder
what is base tilt?
what is it in B-DNA?
upward tilt of base from plane
in B-DNA = -1.2º
what is propeller twist?
what is it in B-DNA?
angle between the base pair and sugar
16º
What is A-DNA? where is usually found?
rare form of double helix seen when less hydrated and in RNA
how is A-DNA different from B-DNA in structure?
major groove is much larger than minor groove
characterstics of A-DNA?
right-handed
11 bp/turn
what is the base tilt and propeller twist of A-DNA?
base tilt: 19º
propeller twist: 18º
what is the width of A-DNA?
2.6 nm
what is the pitch length and base-pair spacing? A-dna
pitch length - 2.5 nm
base-pair spacing - 0.23 nm
How is Z-DNA different?
left-handed helix
has alternating Pu-Py on one side
Pu x-angles are syn
very rare and requires external forces acting on it
less extreme major groove/minor groove compared to A DNA
What causes DNA to flex and utilize its degrees of freedom?
protein interactions, chromatin
where are the degrees of freedom in DNA?
flexibility of the base, base stacking, backbone, transcription, replication
rotation around bonds
deviate from B-DNA
dinucleotides vary in…
structural flexibility based on sequence
What are the 10 differences between DNA and RNA?
- ds vs ss
- no OH vs 2’OH
- thymine vs uracil
- degraded less vs more labile
- permanent vs moew transient
- one function vs varied function
- one major structure vs more varied structure
- longer vs shorter
- chromatin vs no chromatin
- inside nucleus vs inside or outside nucleus
What are the six structural elements of RNA?
what has the sixth type?
- duplexes
- single stranded regions
- hairpins
- bulges
- internal loops
- junctions
tRNA have junctions
most RNA base pairs are
GC or AU but other combinations of non-watson crick are common
RNA base pairs non-Watson-Crick when…
does RNA form similar to B-DNA structure?
ss are across from each other
forced to bp due to proximity form HB (acceptor/donor HBs align)
not standard ds of B-DNA which allow for flexibility
melting/unzipping of base pairs occurs easier
non-Watson Crick base pairing in experimental conditions
what are pseudoknots? when do they occur?
hairpin loop within another hairpin loop
often used by viruses for protection/disguse against host and switches structural conformation when needed
what does pseudoknot structural switching by viruses result in?
different functional properties for the RNA, often involved in ribosome interactions
give RNA unique propoerties: translation (frameshifts, regulation of expression, control of initiation) and general gene expression (especially in viruses)
DNA melting temperature depends on
strand length, sequence and environmental factors
