Nucleic Acids

The difference between the composition of the DNA (deoxyribonucleic acid) molecule and that of RNA (ribonucleic acid) lies in two main aspects. The first concerns the coverage of its five constituent monomers, called heterocyclic bases, whether adenine or guanine, together forming the purines, or cytosine, thymine and uracil, together forming pyrimidines. In RNA, uracil replaces thymine in DNA.

The combination of bases with a molecule of ribose and inorganic phosphate gives rise to nucleosides. . Exemplifying for adenosine, a nitrogenous heterocyclic base in an N-glycosidic bond with the hydroxyl linked to carbon-1 of a ribose (RNA, presence of -OH group at C-2) or deoxyribose (DNA) esterified to a phosphate group. In the same way, guanosine originates, cytidine, thymidine, and uridine.

By assembling interconnected nucleosides, the structure of the biopolymer (DNA or RNA) will be formed by the phosphoester bond between the hydroxyl linked to C5 of the pentose and C3 of the next pentose. The polymeric structure of double-stranded nucleic acids is also maintained by hydrogen bond pairing between G and C (three bonds) and between A and T (two bonds), as follows.

B-DNA

To study the biopolymer, download and load the model of a dodecanucleotide of B-DNA in JSmol/Jmol. Remove the water and show the nucleotide sequence of the double-stranded DNA:

delete water
show sequence

Now represent it as space filled only, and identify the strands separately:

spacefill only
select :A; color red;select: B; color blue

Next, visualize the interior of the double strand and observe the stacking of the DNA base pairs:

select all;wireframe only;wireframe 50
select sidechain;color magenta;select backbone;color blue

Also note that the base pairs are in a horizontal plane, and also perpendicular to the axis of the helix. Note the proximity of the van der Waals interactions:

dots on

Restrict the view to just one base pair, zoom in on it, and notice that the bases induce the slight twisting of the helix, which is important to the structure of DNA, although not identifiable in the Watson-Crick model.

restrict 8 or 7
zoom 0

Also notice the ribose residues, and see that the plane of the residues is perpendicular to the axis of the helix, with no coplanarity between them.

select backbone;color cpk

Which atom of the furanose ring rests above and below its plane? To do this, rotate the molecule so that the phosphate groups of the backbone are on the left, and the plane of the furanose ring is slightly tilted. Note that there is a phosphate bonding below at C3’, as well as above at C5’, forming a 3’-5’ phosphodiester bond.

To visualize the hydrogen bonds of a single base pair, rotate the model after the commands that follow.

restrict 8 or 17
zoom 0
calculate hbonds

And to visualize the hydrogen bonds of the entire structure:

select all;
wireframe only;
wireframe 40;
zoom 0;
calculate hbonds

Note that this visualization allows us to verify the stability of the DNA strand corroborated by its H-bonds in addition to base stacking (hydrophobic)\index{base stacking.

DNA Clefts

Inspect the DNA clefts. Note that the major and minor clefts are defined on the paper plane in a didactic way, from the overlap of the two strands (twist point). To do this, position the double helix perpendicularly and rotate it, to notice that this twist point “walks” through the structure:

select all;
trace only;
spin 10

By definition, the major cleft is always next to the base pairs, while the minor cleft is always next to the furanoses.

A-DNA

Download and load the A-DNA model into Jmol/JSmol. Visualize the single strand of this DNA:

delete water;
select all;
wireframe only;
wireframe 70

Identify the bases and riboses:

select sidechain;
color magenta;
select backbone;
color lightblue

Now observe the A-DNA molecule seen from above, rotating the image or typing:

rotate x 90 # 90 degree rotation on the X axis

Note that there is a channel inside the molecule, which is not present in the B-DNA structure.

Z-DNA

Download and load the Z-DNA structure into JSmol/Jmol. This is a biological construct containing Z-DNA, a structure characteristically rich in GC pairs. To highlight Z-DNA only:

restrict dna;
show sequence;
wireframe only;
wireframe 40

Rotate the molecule and observe that the double strand is formed by a hexanucleotide (GC)\(_{3}\).

Also observe the intercalation of cytidine and guanosine nucleosides in the structure:

select g:A; color red;
select c:A; color blue

The term Z-DNA comes from the zigzag aspect of the orientation of the riboses. Note that from a ribose in blue (below), the phosphodiester bond appears to the left of the phosphorus atom, going up to the other ribose molecule in red, the set forming the zigzag aspect.

Interaction of nucleic acids with ligands

The formation of nucleic acid-ligand complexes will be illustrated by the interaction of a double-stranded RNA with ethidium, using the code DRB018. As you can see, this is an identification external to the PDB. To download this structure, you can visit the Nucleic Acids Database. But you can also load the structure from the ligand-nucleic acid complex.

If you are on the Nucleic Acids Database website, enter the code DRB018 in the search window. Download the resulting coordinate file in the lower corner of the window, under “Assymmetric Unit coordinates”. The file, in the gz attribute, can be opened in Jmol.

Then load the file and render it appropriately:

delete water;
select all;
wireframe only;
wireframe 70

Now rotate the molecule and notice its intercalation between the base stacking of the double-stranded RNA.

Nucleosome

Load the model 1aoi into Jmol/JSmol. It is the central particle of a nucleosome composed of an octamer of histones wrapped in two superhelical turns of double-stranded DNA.

Better identify the structures contained in the nucleosome, separating the protein part from the nucleic part, and rotate the complex to observe its characteristics (DNA-protein interaction envelope).

select protein;cartoon only;color structure
select nucleic;wireframe only;color cpk

Histones interact with DNA mainly through electrostatic interactions with its phosphate groups. To visualize this interaction:

select protein;backbone only;color lightgrey;
select positive; wireframe 80;color green

Transfer RNA

Like proteins, transfer RNA also has primary, secondary and tertiary structures, first evidenced by X-ray diffractometry in 1972. To learn a little more, download and load the t-RNA model, and rotate the structure to see its three-dimensional “L” shape (or cloverleaf, as mentioned in the books). Zoom in and render the structure, outline the coloring from the blue 5’ to the red 3’ terminal, rotate the structure and notice the helical character of the tRNA:

delete water;trace only;color group
zoom 0; zoom 200;wireframe only;wireframe 70

Position the ends on the right (5’ and 3’ ends), and observe the loops that form the secondary structure, the anticodon loop (below), the D loop on the left, and the T and C loops on the right.

More specifically, type the commands below to better visualize the loops:

select 44-48;color red # variable loop
select 10-13 or 22-25;color yellow # stem D

Now observe the parallelism and stacking of the bases along the t-RNA stems:

wireframe only;
wireframe 80;
select backbone;
wireframe

Also select the three anticodon residues for Phe of t-RNA by:

select 36-38; color red

The structure of t-RNA is maintained stable primarily by Watson-Crick base pairing, as well as by H-bonds. To observe this:

select all;
color structure;
calculate hbonds;
hbonds 0.2;
color hbonds black

Stability is also enhanced by H-bond interactions between ribose residues. To observe this:

select nucleic;
wireframe 80;
color green;
restrict backbone;
select(6-8,48-50);
color cpk

Bring the sugar residues closer and notice (by mouse click) that 2’-OH of ribose 7 can form an H bond with O no. 49 of the sugar ring. The length of an H-bond lies between 2 and 4 Angstrom.

To check the potential for forming an H bond between the carbohydrates above, right-click, select “Measurements” (or its translation, if you are in your native language) and “Click for distance measurement”. Now click on the first desired atom (2’-OH) and then on the one that has the potential to form the pairing (O-49). And remember that 1 nm is equal to 10 Angstrom.

In general, the base-base, base-sugar, base-phosphate, sugar-sugar, and sugar-phosphate pairings contribute as H bonds to the stability of t-RNA.

Now visualize a Watson-Crick pairing, albeit with the G and C residues in non-helical portions of the t-RNA, by typing:

select all;color lightgrey;wireframe;hbonds off # model cleaning
select 19 or 56;color red

To observe the importance of base interactions for the tertiary structure of the t-RNA type:

hbonds off;backbone only;
color structure;
select 18 or 55;color orange;
wireframe 100;
hbonds on;hbonds 0.3

tRNA interacts with amino acid transporters by triplets of codons in its structure (or trinucleotides). Highlighting the GGC triplet:

select all;hbonds off;wireframe only;
color lightgrey;select (9,13,22,46);wireframe 80;
color cpk

Ribosomes

For a structural study of ribosomes, download and load the 30S subunit of the ribosome of Thermus thermophilus. Distinguish the nucleic from the protein structures:

cartoon only;select nucleic;color green; select protein;color orange

Is the structure represented “more RNA” or “more protein”? Try to visualize it by rotating the model by:

select all;spacefill only

Is the protein structure unique? To solve this question, rotate the structure from:

select all;select nucleic;color cpk;
select protein;color chains
spin 10

And how does the nucleic part fold?

restric rna

Observe the spherical shape and the nuclear characteristic of the RNA, to which the various proteins that form the 30S subunit are complexed.

70S ribosomal particle

To observe it, download and load into Jmol/JSmol the model of the 70S particle of Thermus thermophilus complexed to m-RNA and t-RNA. Alternatively, you can download the original file 4v42 from Jmol itself. But note that if you try to do it through Menu, Get PDB, you will not be successful. For this model, you need to download the file from the PDB website, in PDBx/mmCIF Format (gz) format. This is necessary because it is a file subdivided into two structures, 30S and 50S subunits. In addition to these, the bacterial ribosome has a hexanucleotide segment of m-RNA complexed with three t-RNAs.

The model shows three t-RNAs inside (blue-red), a large set of proteins (dark gray), and the remaining nucleic structure (orange). The 70S ribosome is quite complex, with several sites, both for interaction with t-RNA (A, P and E) and for interaction with protein subunits. To find out how many of these, type show info, and you will see that the structure has 49 polypeptide chains. At the terminal part of t-RNAs, the nearby A and P sites define the site of peptidyl transferase activity on the ribosome.