Nucleic acids Molecular biology and physics, Structure of nucleic

acids, Intra-molecular interactions in the double helix

Mitesh Shrestha

Molecular biology and physics

• Density-gradient centrifugation of DNA

• X – Ray Crystallography for determination of structure of macromolecules

• Ramachandran Plot for structure prediction of Proteins

Structure of nucleic acids

• DNA or RNA

– Nitrogenous Bases

– Deoxyribose or Ribose Sugar

– Phosphate

Organic “bases” in DNA (& RNA):

Organic “bases” in DNA (& RNA):

Sugar-phosphate backbone in DNA & RNA:

Nature Magazine VOL 171, page737; 2 April 1953:

MOLECULAR STRUCTURE OF NUCLEIC ACIDS

A Structure for Deoxyribose Nucleic Acid

We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This

structure has novel features which are of considerable biological interest.

A structure for nucleic acid has already been proposed by Pauling and Corey (1).

They kindly made their manuscript available to us in advance of publication. Their

model consists of three intertwined chains, with the phosphates near the fibre axis,

and the bases on the outside. In our opinion, this structure is unsatisfactory for two

reasons: (1) We believe that the material which gives the X-ray diagrams is the salt,

not the free acid. Without the acidic hydrogen atoms it is not clear what forces would

hold the structure together, especially as the negatively charged phosphates near the

axis will repel each other. (2) Some of the van der Waals distances appear to be too

small.

http://www.nature.com/genomics/human/watson-crick/

We wish to put forward a radically different structure for the salt of

deoxyribose nucleic acid. This structure has two helical chains

each coiled round the same axis (see diagram). We have made the

usual chemical assumptions, namely, that each chain consists of

phosphate diester groups joining ß-D-deoxyribofuranose

residues with 3',5' linkages. The two chains (but not their bases)

are related by a dyad perpendicular to the fibre axis. Both chains

follow right- handed helices, but owing to the dyad the sequences

of the atoms in the two chains run in opposite directions. Each

chain loosely resembles Furberg's model No. 1; that is, the bases

are on the inside of the helix and the phosphates on the outside.

The configuration of the sugar and the atoms near it is close to

Furberg's 'standard configuration', the sugar being roughly

perpendicular to the attached base. There is a residue on each

every 3.4 A. in the z-direction. We have assumed an angle of 36°

between adjacent residues in the same chain, so that the structure

repeats after 10 residues on each chain, that is, after 34 A. The

distance of a phosphorus atom from the fibre axis is 10 A. As the

phosphates are on the outside, cations have easy access to them.

The novel feature of the structure is the manner in which the two

chains are held together by the purine and pyrimidine bases. The

planes of the bases are perpendicular to the fibre axis. They are

joined together in pairs, a single base from the other chain, so that

the two lie side by side with identical z-co-ordinates. One of the

pair must be a purine and the other a pyrimidine for bonding

to occur. The hydrogen bonds are made as follows : purine

position 1 to pyrimidine position 1 ; purine position 6 to

pyrimidine position 6.

If it is assumed that the bases only occur in the structure in the

most plausible tautomeric forms (that is, with the keto rather than

the enol configurations) it is found that only specific pairs of

bases can bond together. These pairs are : adenine (purine) with

thymine (pyrimidine), and guanine (purine) with cytosine

(pyrimidine).

In other words, if an adenine forms one member of a pair, on

either chain, then on these assumptions the other member must

be thymine ; similarly for guanine and cytosine. The sequence

of bases on a single chain does not appear to be restricted

in any way. However, if only specific pairs of bases can be

formed, it follows that if the sequence of bases on one chain

is given, then the sequence on the other chain is

automatically determined.

It has been found experimentally that the ratio of the

amounts of adenine to thymine, and the ratio of guanine to

cytosine, are always very close to unity for deoxyribose

nucleic acid.

It has not escaped our notice that the specific pairing we have

postulated immediately suggests a possible copying

mechanism for the genetic material.

DNA Double Helix:

Types of DNA structure

B – DNA

• The structure of B-DNA was elucidated by Watson and Crick 6 in 1953. The B-DNA is composed of two complementary strands running in opposite direction held together by hydrogen bonds between base pairs. It is generally believed that DNA in prokaryotic and eukaryotic cells exists in the B-form. B-DNA is less compact than the A-form containing 10 base pairs versus 11 per turn of helix.

• Both A- and B-forms are right-handed double helices. In contrast Z-DNA is a left-handed duplex . The base pairs of B-DNA are perpendicular to the helical axis.

• The radius of the helix is roughly 10 ‎Å. The base pairs have about 12° torsional twist relative to each other. The phosphate groups which are on the outside of the B-DNA are highly charged and are presumed to interact with positive ions and water.

A – DNA

• The physiological B-form can be converted into A-DNA by increasing the salt concentration.

• Under appropriate conditions the A-form is more stable than B-DNA. ADNA is structurally homologous to the double-stranded RNA, the major groove being almost flush with the surface of the molecule and the minor groove being deep.

• This conformation has eleven base pairs per turn and the base pairs are tilted by about 20° relative to the perpendicular base pairs of B-DNA.

• The base pairs are not quite coplanar showing 15° of propeller twist. The physiological salt concentration would not allow the existence of A-form. Its biological role is not clear but possibly may occur upon association with proteins specific to DNA.

Z - DNA • This conformation was discovered by Rich and his associates in

concentrated salt solutions when the bases G and C were strictly alternating.

• The (G-C), sequence allows a novel type of secondary structure which is left-handed.

• The backbone of Z-DNA is a zig-zag with a double nucleotide pair repeat, unlike the sinuous S-curve in the backbone of A and B-DNA.

• The base-pair propeller twist in Z-DNA is minor: the base pairs are slightly tilted (10°) and virtually coplanar in contrast to A and B-DNA.

• The minor groove of Z-DNA is very deep and the major groove is shallow in this structure.

• The existence of Z-form in nature has been demonstrated recently. Antibodies raised against Z-DNA are bound to polytene chromosomes H confirming its natural existence.

RNA is “ribonucleic acid.” It differs from DNA in the type of sugars it contains and its base composition.

• The ribose sugars in RNA contain a hydroxyl group at the #2 ring position. (DNA does not.)

• Uracil is present in RNA instead of Thiamine found in DNA.

• Most often RNA is single-stranded.

• RNA is found throughout the cell, while DNA is normally confined to the nucleus and some other organelles in eukaryotes.

• RNA molecules of various lengths and composition perform different duties in the cell.

Types of RNA:

• Messenger RNA (mRNA) – template for protein synthesis (“translation”)

• Transfer RNA (mRNA) – transports amino acids in activated form to the ribosome for protein synthesis.

• Ribosomal RNA (rRNA) – Major component of ribosomes, playing a catalytic and structural role in protein synthesis.

RNA Transcription

• All RNA synthesis is catalyzed by “RNA polymerase.”

• RNA polymerase requires: – A template (a double or single strand of DNA)

– Activated precursors (ATP, UTP, CTP, GTP)

– A divalent metal ion (Mg2+ or Mn2+)

• RNA polymerase binds to double stranded DNA and causes an unwinding and separation of the double helix.

• When a “promotor site” is encountered on the DNA, it begins transcribing RNA by catalyzing the formation of phosphodiester bonds between the ribonucleoside triphosphates in a similar fashion to DNA synthesis.

• RNA polymerization stops at “termination sites” located on the DNA that are recognized by RNA polymerase.

RNA Polymerization

tRNA Structures

Secondary Structure Tertiary Structure

Intra-molecular interactions in the double helix

• Various Weak Forces come together to stabilize the DNA structure.

– Hydrogen bonds, linkage between bases, although weak energy-wise, is able to stabilize the helix because of the large number present in DNA molecule.

Intra-molecular interactions in the double helix

Intra-molecular interactions in the double helix

• Various Weak Forces come together to stabilize the DNA structure. – Stacking interactions, or also known as Van der Waals interactions

between bases are weak, but the large amounts of these interactions help to stabilize the overall structure of the helix. • Double helix is stabilized by hydrophobic effects by burying the bases in the

interior of the helix increases its stability; having the hydrophobic bases clustered in the interior of the helix keeps it away from the surrounding water, whereas the more polar surfaces, hence hydrophilic heads are exposed and interaction with the exterior water

• Stacked base pairs also attract to one another through Van der Waals forces the energy associated with a single van der Waals interaction has small significant to the overall DNA structure however, the net effect summed over the numerous atom pairs, results in substantial stability.

• Stacking also favors the conformations of rigid five-membered rings of the sugars of backbone.

Intra-molecular interactions in the double helix

• Various Weak Forces come together to stabilize the DNA structure.

– Charge-Charge Interactions- refers to the electrostatic (ion-ion) repulsion of the negatively charged phosphate is potentially unstable, however the presence of Mg2+ and cationic proteins with abundant Arginine and Lysine residues that stabilizes the double helix.

Intra-molecular interactions in the double helix

• Considering the forces involved in DNA packaging – strong electrostatic repulsion between negatively charged phosphate groups, the loss of DNA configurational entropy, and deformation of the stiff DNA helix – there is no surprise that organisms expend substantial metabolic energy to accomplish the task.

• It has been estimated that about one ATP molecule is hydrolysed per two base pairs packaged.

• On the other hand, in vitro DNA condensation can occur spontaneously upon addition of low concentration of multivalent ions.