MBB wk3-1 duplex stability

what are the 3 types of non-covalent interactions in duplex

• ionic interactions

• H-bond

• van der Waals interactions 

where can you find ionic interactions in duplex

it is the repulsion between charged backbone phosphates

where can you find H-bonding in duplex

between the complementary bases in opposite strands

are nucleic acids hydrophilic or hydrophobic

hydrophilic

why do nucleic acids have high aq solubility

due to most of their covalent bonds being polar

what happens when bond dipoles have partial charges 

bond electrons are unequally shared 

why do two strand backbones in a duplex repel each other

because both backbones contain a phosphate group w/ a negative charge, so they repel each other

what holds the two strands together

nucleobases w/ H-bonds

what is the beer lambert law

absorbance = e (extinction coefficient) x c (concentration) x l (light path length)

do duplexes absorb more or less UV than single strands

less

what is the hyperchromic effect 

separating two strands of a duplex from low temp to high temp increases its UV absorption

what is the hypochromic effect 

combining two strands into a duplex from high temp to low temp decreases its UV absorption 

what is Tm

melting temperature, the value of T where 50% of the DNA is denatured

does higher extinction coefficient = more or less UV absoprtion

more UV absorption

does higher Tm = more stable or less stable

more stable

does higher salt concentration in a solution = more stable or less

higher salt concentration = higher Tm = mores stable

why does higher salt concentration = more stable 

Na+ ions neutralize negative charges on the phosphate groups to stabilize the duplex 

does longer duplex = more or less stable

longer duplex = higher Tm = more stable

does mutation = more or less stable

mutation = lower Tm = lower stability

what does it mean for a mutation

changing a nucleobase → disrupts a base pair

when are H-bonds the strongest

when the donor, H, and acceptor are in a straight line (180 degrees)

are H bonds direction-dependent

yes

does the strength of ionic interactions depend on the orientation

no!

which pair is more stable G:C or A:T

G:C

why are G:C pairs more stable

they have stronger london interactions and aromatic stacking

why do G:C pairs have stronger london interactions

they have more co-planar atoms than A:T pairs, therefore stronger london interactions

why do G:C pairs have stronger aromatic stacking

they have stronger aromatic stacking attraction between pi-electron clouds

why do ionic repulsion of phosphate groups favour separation

because the negatively charged phosphate groups repel each other, weakening the attraction between the two strands, favouring separation