Conformation, Base Pairing and Base Stacking

How are conformations of nucleotides defined?

1. resonance structures of bases

2. rotation of base relative to sugar

3. phosphate backbone torsion angles

4. sugar pucker (distortion out of plane)

How many torsion angles per nucleotide?

7 total (6 in phosphate backbone and the glycosidic bond)

How are conformations of nucleotides defined?

1. resonance structures of bases

2. rotation of base relative to sugar

3. phosphate backbone torsion angles

4. sugar pucker (distortion out of plane)

How many torsion angles per nucleotide?

7 total (6 in phosphate backbone and the glycosidic bond)

Two types of sugar puckers

Endo and Exo

Most common conformation of DNA

B-form

Sugar pucker of B-form DNA

C2’-endo

what do ring conformations influence

reactivity, base-pairing potential, recognition

Syn vs anti base conformation, where are they found

Syn and anti conformations refer to the orientation of the bases in nucleic acids, with syn bases faing towards the sugar and anti facing away. Pyrimidines only have anti-conformation due to steric hindrance. Purines can adopt both syn and anti conformations but favour syn dlightly due to a favourable electrostatic conformation between phosphate anion and amino group

In B-DNA is the major or minor groove more negatively charged

minor, the opposite is true in A-form due to the bend over of phosphates into the major grooveThe minor groove in B-DNA is more negatively charged, while in A-form, the major groove is more negatively charged due to the bending of phosphates.

What binds to the regions of extreme potential

protons, metals, proteinsthat interact with nucleic acids.

Why is DNA predominantly in B-form structyre?

because it readilt adopts the C2’-endo pucker

why does double-stranded RNA form a similar structure to A-from

The ribose is locked into a C3’-endo pucker

charge of DNA components at pH 7

bases and pentoses are uncharged and unreactive

Which atoms act as H-bond acceptors/donors

in nucleobases, typically O and N atoms.

How is H bonding gspecificity determined

steric factors and the number of bonds formed

Hoogsteen base pairing

is a type of base pairing in nucleic acids that occurs between nucleobases through specific hydrogen bonds, differing from traditional Watson-Crick base pairing. Leads to a smaller C-1 to C-1 distance and a larger anglebetween the paired bases, allowing for alternative structures in DNA and RNA.

Why are wobble pairings important

allows for degeneracy in the genetic codeby enabling multiple codons to code for the same amino acid.

How are base triples formed

unse hoogsteen to bind antisense oligos to dsDNDA and stabilize the formation of triplex structures in nucleic acids, providing additional regulatory mechanisms in gene expression.

When are non-WC base pairing significant

1. anticodon and codon pairing

2. forming triple-stranded helices

3. in the compact RNA structure to maximize base pairing and stacking

4. as recognition sites for enzymes

Base flipping

one base is flipped at a time allowing enzymes to methylate bases or remove damaged bases

What force drives base stacking

van der waals

Why dont mononucleotides in aqueous solution base pair

no enthalpic benefit from H-bonds between bases becuase water filled those spots. base staking is more favourable because the bases are hydrophobic, mononucleotides form stacks

how does UV absorption change with denaturation

As DNA denatures, UV absorption increases due to the exposure of more bases, leading to hyperchromicity. Stacked bases absorb less light

What provides free energy for nucleic acid hybridization

base stacking

What provides specificity and some free energy

hydrogen bonding

is entropy more important for protein folding or nucleic acid strucuture