Nucleic Acid Structure

Question 1

What are the forces that influence nucleic acid structure?

Answer 1

base stacking, base pairing, ionic interactions

applies to DNA and RNA

Question 2

Which force influences DNA stability the most?

Answer 2

base stacking

base pairing HB is important for structure but less in stability

Question 3

base stacking depends on…

Answer 3

sequence-dependent

order matters: AT vs TA on top

Question 4

What is base stacking?

Answer 4

induced dipole and partial charge interactions between rings of bases (nitrogen atoms)

PI BOND STACKING

Question 5

∆G of stacking is

Answer 5

the stability of base stacking; equilibrium of free energy btwn ss vs ds

more -ve = more stable

Question 6

Which bases affect ∆G of stacking more?

Answer 6

G’s and C’s make more -ve = more stable
-> when G is on top of C

GC*GC -> -2.17

Question 7

why is base stacking sequence dependent?

Answer 7

different charge and hydrophobic interactions result

hydrophobic groups together and opposite partial charges together

Question 8

ss nucleic acid has higher ∆G because

Answer 8

no base stacking bc no base pairing
-> HB present with water

Question 9

What is the advantage of ds to ss in HB?

Answer 9

ds = HB between bases
ss = HB between base and H2O

ds advantage = cooperativity

Question 10

What are ionic interactions?

Answer 10

cations shield repulsion between negative phosphates

Question 11

what are cation-DNA interactions mediated by?

Answer 11

H2O

Question 12

What are the better cation shielding agents?

Answer 12

divalent (Mg2+) over monovalent (Na+, K+)

Question 13

What does a DNA melting curve show?

Answer 13

increase in absorbance as temperature increases

higher GC content -> higher melting temperature

Question 14

What are the 5 factors that influence DNA stability?

Answer 14

1. length and sequence of DNA strands
2. degree of complementarity
3. nature of solvent
4. [] and types of ions present
5. pH

Question 15

equation for melting temperature?

Answer 15

Tm = 2(A+T) + 4(G+C)

Question 16

what is the effect of complementarity on DNA stability?

Answer 16

mismatches have steric effects -> pur-pur = lose helix and base stacking

Question 17

What is intra-base pair coordinates?

Answer 17

movement of bases; degree of freedom between HB bases

Question 18

What are the types of intra-base pair coordinates?

Answer 18

1. shear
2. buckle
3. stretch
4. propeller
5. stagger
6. opening

Question 19

what are inter-base pair (step) coordinates?

Answer 19

base stacking that gives DNA flexibility to interact w/ other proteins

Question 20

Why does DNA form a double helix?

Answer 20

• 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

Question 21

What are the dimensions of a base pair?

Answer 21

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

Question 22

Why is the space between base pairs on top of each other 2.6Å?

Answer 22

space is large enough for water to fit through

Question 23

bases are pushed together because…

Answer 23

water forms ordered networks around the hydrophobic regions -> unfavourable entropy

minimize water - hydrophobic interaction

Question 24

Why must there be a space between base pairs on top of each other?

Answer 24

steric hinderence of phosphate backbones due to inflexibility

Question 25

why can't we have stair-like structure of DNA? | side by side or front and back

Answer 25

a lot of exposed hydrophobic bases area | this is why we need a TWIST -> helix

Question 26

what is the pitch length?

Answer 26

length of 1 complete turn of B-DNA 3.4 nm

Question 27

average or ideal B-DNA double helix is

Answer 27

10 bp/turn right-handed | lowest energy conformation

Question 28

what is the width of B-DNA? what does it include?

Answer 28

~2 nm/20Å from phosphate to phosphate

Question 29

if you look down a helix...

Answer 29

it is a perfect cylinder

Question 30

what is base tilt? | what is it in B-DNA?

Answer 30

upward tilt of base from plane | in B-DNA = -1.2º

Question 31

what is propeller twist? | what is it in B-DNA?

Answer 31

angle between the base pair and sugar | 16º

Question 32

What is A-DNA? where is usually found?

Answer 32

rare form of double helix seen when less hydrated and in RNA

Question 33

how is A-DNA different from B-DNA in structure?

Answer 33

major groove is much larger than minor groove

Question 34

characterstics of A-DNA?

Answer 34

right-handed 11 bp/turn

Question 35

what is the base tilt and propeller twist of A-DNA?

Answer 35

base tilt: 19º propeller twist: 18º

Question 36

what is the width of A-DNA?

Answer 36

2.6 nm

Question 37

what is the pitch length and base-pair spacing? A-dna

Answer 37

pitch length - 2.5 nm base-pair spacing - 0.23 nm

Question 38

How is Z-DNA different?

Answer 38

left-handed helix has alternating Pu-Py on one side Pu x-angles are syn | very rare and requires external forces acting on it ## Footnote less extreme major groove/minor groove compared to A DNA

Question 39

What causes DNA to flex and utilize its degrees of freedom?

Answer 39

protein interactions, chromatin

Question 40

where are the degrees of freedom in DNA?

Answer 40

flexibility of the base, base stacking, backbone, transcription, replication | rotation around bonds ## Footnote deviate from B-DNA

Question 41

dinucleotides vary in...

Answer 41

structural flexibility based on sequence

Question 42

What are the 10 differences between DNA and RNA?

Answer 42

- 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

Question 43

What are the six structural elements of RNA? | what has the sixth type?

Answer 43

1. duplexes 2. single stranded regions 3. hairpins 4. bulges 5. internal loops 6. junctions | tRNA have junctions

Question 44

most RNA base pairs are

Answer 44

G*C or A*U but other combinations of non-watson crick are common

Question 45

RNA base pairs non-Watson-Crick when... | does RNA form similar to B-DNA structure?

Answer 45

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 ## Footnote

Question 46

melting/unzipping of base pairs occurs easier

Answer 46

non-Watson Crick base pairing in experimental conditions

Question 47

what are pseudoknots? when do they occur?

Answer 47

hairpin loop within another hairpin loop often used by viruses for protection/disguse against host and switches structural conformation when needed

Question 48

what does pseudoknot structural switching by viruses result in?

Answer 48

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)

Question 49

DNA melting temperature depends on

Answer 49

strand length, sequence and environmental factors