Nucleic Acids-RNA-DNA

3 parts of nucleic acids

• sugar

• phosphate

• base

Which sugar does RNA use?

beta-D-ribose

Which sugar does DNA use?

beta-D-deoxyribose

which sugar is this & in which structure we can find it

beta-D-ribose

RNA

which sugar is this & in which structure we can find it

beta-D-deoxyribose

DNA

base + sugar

nucleoside

base + sugar + phosphate

nucleotide

Which strand carries genetic info?

sense (coding) strand

Which strand is used as a template for RNA?

antisense (non-coding) (complementary) strand

What is the name of the bond between sugar and base?

Glycosidic Bond

sugar conformation preferred by DNA?

C2’-endo

sugar conformation preferred by RNA?

C3’-endo

What causes unusual DNA helices in purines?

favourable interaction between N2 and 5’-PO42- that stabilizes the syn conformation

isomers that differ in the location of protons (and consequently double bonds)

tautomers

How do polynucleotides form if unfavourable?

Coupling with favourable reactions

Does RNA takes on more varied shaped and folding patterns than DNA?

Yes

2 reasons why non-coding RNA structure is less constrained than DNA structure

1. More no=umbers of building blocks (modified bases and sugars)

2. Non standard base pairing

a non-standard base pair that differs in geometry relative to the standard, Watson-Crick-Rosalind pairing

wobble

common non-standard base pair type

G-U

alternative H-bonding pattern that uses different faces of the base

Hoogsteen base pairing

Which configuration is favoured for base pairs along the Hoogsteen edge?

trans

Which configuration is favoured for base pairs along the Watson-Crick-Rosalind edge?

cis

How RNA stabilizes its secondary structure?

The negative backbone forces the bases to interact (pair&stack)

What prevents the formation of B-type dsRNA helices?

C3’ -endo conformation of RNA ribose

the intersection of 3 or more ssRNA, sometimes resulting in separation of the helices by unpaired residues

junctions

most common junction seen in RNA

three-stem

secondary structure of RNA composed of unpaired nucleotides within 1 strand of a base-paired region of RNA, and can be as short as a single base

bulge

Which secondary structure is associated with metal binding or cationic ligand binding?

bulge

This secondary structure occurs when there are unpaired nucleotides on both sides of dsRNA.

These can be symmetric or asymmetric.

internal loop

Which secondary structure of RNA result in sharp turns and kinks due to induced unwinding & critical for tertiary structures?

internal loop

This secondary structure is formed when the RNA folds sharply back onto itself, with the loops ranging in size from 2-14 residues.

hairpin loop

How hairpin loop stabilize the structure?

With its base-pairing and pi-pi stacking

What is GNRA tetraloops?

loops composed of the 4 bases:

G: guanosine

N: any base

R: purine

A: adenosine

What type of secondary structure are GNRA tetraloops?

type of hairpin loop

In this type of interactions, when 2 regular helical elements (A-type) stack end-t-end, they form a coaxial stack.

dsRNA - dsRNA interactions

How dsRNA-dsRNA interactions stabilize the tertiary structrure?

The base pair at the end of one helix can undergo pi-pi stacking interactions with the opposite base pair of the next helix.

Which type of interactions form pseudoknots?

ssRNA-ssRNA interactions

These are coaxial helical stacks of 2 helices that are discontinuous to each other

pseudoknots

How do pseudoknots form?

They form where unpaired nucleotides in the loop of a hairpin form base pairs with a distal complementary stretch of ssRNA.

clusters of 3 RNA nucleobases interacting along their edges via H bonds

base triples

What type of interactions occur most often in the form of base triples?

dsRNA-ssRNA interactions

What type of pairing is a form of base triple?

Hoogsteen pairing

What is A-minor motif?

the interactions of the minor groove edges of adenine with the minor groove of neighbouring helices

minor groove edge = sugar edge

A minor motifs involve _______ interacting with the minor groove of ______, resulting in H-bonding & stacking of the ______

A-minor motifs involve polyA ssRNA interacting with the minor groove of dsRNA, resulting in H- bonding & stacking of the polyA