Structure of nucleic acids, Biology tutorial

Introduction:

Nucleic acids including both RNA and DNA have peculiar structures that are different from one another. Structure of nucleic acids is mainly derived from respective nucleotides for RNA, deoxyribonucleotides for DNA and phosphate acid molecule embedded in structure of different types of nucleic acids and their properties.

Structure of DNA:

  • Structure of DNA was worked out by bringing together the number of observations from different sources. Following are some of the main observations.
  • That DNA from different sources have amazing similarity in Xray diffraction patterns; suggesting that DNA molecules contain uniform molecular pattern and comprises polynucleotide chains arranged in helical structure.
  • That ratio of bases (A: T and C: G) is very close to one. Significance of the observation in working out structure of DNA is that it suggests pairing of bases in DNA helix. It was then illustrated that A and T can be paired with the maximum of two hydrogen bonds between them while C and G will have the maximum of three bonds.
  • Third observation was that of titration data which suggested that long polynucleotide chains were held together by bonds between the residues.

Watson-Crick Model comprise of 2-deoxyribonucleotides attached together by phosphate diesters with bases projecting perpendicularly from chains in central axis. For each adenine projecting inwards, there is the corresponding thymine from other chain and for each cytosine, there is guanine. Therefore A-T and C-G are held together by two and 3 hydrogen bonds respectively. Two chains are though not identical due to base pairings. Chains don't run in same direction with respect to linkage between nucleotides, rather they are antiparallel.

2162_DNA-structure.jpg

Various forms of DNA:

Structurally, there are three different forms of DNA

1) A DNA:

The A form of DNA is favored in a right handed helix with a diameter approximately 26Å. It has 11base pairs per helical turns and rise per base pair is 2.6Å

479_A DNA.jpg

 2) BDNA:

B DNA is also refered to as Watson-Crick DNA structure. DNA is arranged as the left handed helix with estimated diameters of 20Å. Base pairs per helical turns are 10.5 and base turns rise of helix 3.4Å.

1407_B DNA.jpg

3) Z-DNA:

The Z-DNA is a more radical departure from B-DNA with left handed helical rotation. There are 12 base pairs per helical turn, and its structures appear to be more slender and elongated.

811_Z DNA.jpg

Structure of RNA:

1) Primary structure:

RNA molecule is generally an unbranched linear polymer having nucleotides as its monomers that are generally joined by phosphodiester linkage. Modification of bases of RNA happens generally after polymerization and adds to some structural features of RNA molecule like 5' terminus 7 methyl cap in eukaryotic mRNA. Linkage of ribonucleotides in RNA is 3'5' phosphodiester link involving 3'-OH group of ribose and 5'-phosphate group of another ribonucleotide. This linkage forms backbone from which chains are extended. Length of RNA molecule in eukaryotes is from 65 nucleotides to 6000 nucleotides.

2) Secondary structure:

RNA in solution shows greater varieties of structures. In low ionic strength solutions, molecules appear as extended polyelectrolyte chains while in high ionic strength solutions they contract. The single strand of RNA may contain double helical regions created by hydrogen bonding between complimentary base sequences within RNA molecule. These double helical regions may or may not contain large unpaired loops at end as shown in tRNA.

3) Tertiary structure:

RNA in solution is dynamic molecules in solution. They suffer changes in conformation in synthesis, processing and functioning. Association of RNA with proteins allows RNA molecule to be stable and also fold in specific conformations like "L shaped" conformation of tRNA. Arms and loops of tRNA are folded in specific conformations held in position not only by base pairing interactions but also other interactions. This folding which happens in tRNA molecule apparently happens during functioning like during transcription

Structure of different kinds of RNA:

Structures of the three major kinds of RNA namely: mRNA, tRNA and rRNA.

1) Messenger rna (mRNA):

Messenger RNA (mRNA) particularly eukaryotic mRNA has some exclusive structures not found in rRNA or tRNA. Structurally, 5'terminus mRNA is "capped" i.e. its 5' end being covered with the methylated base particularly (Guanosine 5' triphosphate). Methylation is on 2'-hydroxyl group of ribose sugar. Capping is followed by the non translated or "leader" sequence. Following leader sequence is initiation codon or sequence, most frequently AUG . Coding region follows non-translated region of mRNA molecule. At the end of coding sequence, termination sequence is found. Second non translated sequence follows, that is terminated by series of adenylic acids known as poly A tail that makes up 3' terminus of mRNA molecule.

2) TRANSFER rRNA (tRNA):

Transfer RNAs range in length from 65-110 nucleotides that corresponds to molecular weight of 22, 000-37500 Daltons. Sedimentation coefficient for tRNAs as group is 4S. Letter, S (Svedberg) in 4S is frequently utilized to designate unit of tRNA. Structurally, tRNAs have high proportion of altered nucleotides and bases engaged in secondary conformation, helices and tertiary folding which makes them to conform to general 2 dimensional cloverleaf structure or three dimensional L-form as found by x-ray crystallography. tRNA is single stranded 5' to 3' nucleotide stretch folded in conformation with different loops consequently of intramolecular hydrogen bonding of base pairs within molecule. Different loops are: D-loop, anticodon loop, variable loop or arm, TψC loop and acceptor system, each containing its own function.

3) Structure of ribosomal RNA(rRNA):

Structurally rRNA has the helical structure resulting from folding back of single stranded polymer but may exist in numerous conformations.

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