DNA molecular interactions

$($a$)$ Draw the $5\text{'}-$monophosphate$-2\text{'}-$

deoxythymine $($dT$)$ nucleotide

covalently bonded with neighboring

DNA nucleotides, similar to the

chalkboard drawing for

$5\text{'}-$monophosphate$-2\text{'}-$

deoxyadenosine $($see figure$).$

$($b$)$ Include hydrogens for the

hydrogen bond donating groups of

the base

$($c$)$ Add lone pair electrons for

hydrogen bond accepting groups of

the base

$($d$)$ How many hydrogen bonds can

the base group make with any partner, including water?

$($e$)$ How many VDW contacts can the base make with any partner? Hint: Each atom can

make a good VDW contact.

$($f$)$ Compare these numbers for hydrogen bonds and VDW contact and multiply by typical

energy values $(k\frac{J}{m}ol)$ for each interaction. Which contributes more to stabilizing

molecular interactions?

$($g$)$ Compare your values for VDW and hydrogen bonds to the repulsion of two

phosphate groups in DNA separated by $8.$ Show your work to compute the energy of

this electrostatic interaction.