6 Sequences dictate structures and some unusual structural motifs in DNA

Prof. Sunil Kumar Khare

Introduction

 

DNA is a building block of genetic information passes from parents to the offspring. DNA is present in double helical form. There are four bases present in DNA and the arrangement of these four bases give rise to the different pattern in DNA double helix. The structure of DNA totally depends upon the sequences of these bases which can give a hint to identify their function in the organism. It is well known fact that DNA can attain various conformations locally and globally depending upon the nucleotide sequences and environment conditions. Albeit, the environmental conditions can be fluctuated, the probable structure of the DNA can be predicted by DNA sequences. These sequences also help us to anticipate the DNA structure. Infect, physical parameters responsible for the alteration of DNA structure could be calculated form the DNA sequence. Three such examples of physical parameters are intrinsic curvature, position preference and stacking energy.

 

Intrinsic DNA curvature

 

DNA which is intrinsically curved in the solution is called intrinsic DNA curvature. It can identified by inconsistently very slow migration on polyacrylamide gels. Their structure is unusual and different from the canonical B-DNA structure. A good example of this kind of DNA structure is A-tract DNA structure. Numerous mockups have been anticipated to define A -tract structure and how it is responsible for the deflection of the DNA helical axis.

 

Position preference

 

It refers to the anisotropic DNA flexibility. It is a model altered by three nucleotide (trinucleotide). The alteration in the flexibility occurs by their presence in nucleosomal core sequence.

 

Stacking energy

Stacking energy value can be calculated from dinucleotide value. A positive peak in base-=stacking reflects a region which melts more easily.

 

In addition, DNA can take numerous conformations due the presence of different arrangements of nucleotide sequence and variable energy states. Several DNA structures and motifs are worth to mention here.

 

Unusual structural motifs in DNA

 

Both Single-stranded DNA and double-stranded DNA can possibly adopt a wide range of unusual motifs be it duplex or hairpin. Quite a few ideologies have been proposed for the creation of these unusual structures. These principles have been established by observing the number of recurring structural motifs formed in response to the variation in sequences. These include:

 

(i)     Inside loops of successive mismatches in a B-DNA duplex formed after shearing of base pairs present head-to-head to confer excessive cross- and intra-strand stacking.

(ii)   Zipper like duplex (crossed like fingers) formed when trimmed G´A base pairs are parted by pairs of purine´purine mismatches.

(iii) Stacking is not confined to base even deoxyribose has ability to do so.

(iv)  The G´C and A´T base pairs are much more flexible to attain significant deviations from normal H-bonded conformation. When sheared G´A base pairs bracketed the paired bases become stacked and arrange perpendicularly to the near by bases in the company of interacting drugs.

(v)    The loop structures which are rich in purine and pyrimidine are remarkably diverse in their nature. Although, the purine rich loops may form tri loop structures locked by a sheared G´A, A´A, A´C. Conversely, the pyrimidine rich loops having a thymidine at first position could not do base pairing. However, the thymidine residue could fold inside the minor groove in order to form a compressed loop.

Furthermore, with established G´C and A´T base pairs, several sequences of DNA assume a number of infrequent constructions in any of the double or single stranded state. For instance, the (CG) 2 repeats take up the left-handed Z-DNA structure. The presence of these kind of structures in vivo has been shown in recent times by the detection of proteins that has specificity for the left-handed double helix. Likewise, the G-rich ssDNA sequences both in vivo and in vitro can assume G-tetrad quadruplex structure. As eukaryotic system is rich in tandem repeat sequences it is of great interest to identify the unusual structures adopted by these repeat sequences. Moreover, ssDNA studied by the SELEX technology may adapt 3D structures (aptamer) in order to align with the target molecules. Besides this the ssDNA virus or plasmid comprise an strange foldback structure near the 3’ end so as to bring replication process to an end. These kind of unusual structural motifs could be a potential targets for pharma research. Further, in this topic we will describe the formation of these structures one by one.

 

Internal loop motifs

 

Formation of internal loop motif occurs due to two or four mismatched base pairs in DNA duplexes. These unusual duplexes are less stable than the canonical G´C or A´T base pairs and their degree of instability depends on the nature of incorporated mismatch base pairs. However, tandem sheared purine´ purine and purine´ pyrimidine base pairs are the exemptions to this rule Fig. 1. The schemes of the sheared G´A pairing and its extension to the A´A and A´C are shown in Fig. 1. These kind of base pairing is totally different from the normal Watson and crick base pairing with respect to the H – bonding. For instance, a purine base present in the minor groove can use its functional groups to pair with the functional groups of purine or pyrimidine base in major groove to form the sheared pairing.

Examples of internal loop motifs are 2 X 2 (GA)2 internal loops, 2 X 2 (GC)/(AA) internal loops, 4 X 4 internal loops

 

a). 2 X 2 (GA)2 internal loops

 

These kind of internal loops are only found in B-DNA and A-RNA duplex. However, it is still not clear what are the possible reasons behind this behavior. But, it may be due to the fact that a single sheared base pairing causes the substantial backbone torsion angle distortions and interrupts the canonical intra-strand base stacking in the B-DNA duplex. Therefore, single sheared G´A pair is not favored and it require two such sheared base pairs (a 2 X 2 internal loop) in tandem.

 

b). 2 X 2 (GC)/(AA) internal loops

 

Recently, it was observe that hetero purine/purine (G/A) and purine/pyrimidine (A/C) cross -strand base stacking also exists. It was found in the human HIV-1 reverse transcriptase DNA inhibitor. The paired bases and bases were found to contribute in sheared pairing.

 

c). 4 X 4 internal loops

 

The 2X2 internal loop has very good property of stable intra-strand stacking in the sheared base pairs and even with their neighbor base pairs. Looking into this scenario it became possible to construct 4X4 internal loop, provided the surrounding of mismatch base pairs can provide good intra-strand stacking.

 

Figure 1. Paring of sheared bases

Zipper like motifs

 

The first zipper-like motif was revealed in human centromeric tandem repeats. It was purine rich (TGGAA)n strand and display same thermal stability as that of canonically DNA duplex. Thus, we can believe that these strands separate and have very important biological functions.

 

Examples of zipper like motif are as fallows:

  1. 5’-GGA/AGG-5’ motif.

The remarkable feature of this motif is that the middle guanosine residues are not paired but intercalated with each other. These unpaired guanosine then participate in stacking arises in response to G´A pairs. As a result large upfield shifting of the H4’ proton of the unpaired guanosine residue takes place. Another interesting fact is that as guanosine residue is free so the NH2 group can form H-bonding with the cross-strand phosphate backbone.

  1. 5’GGGA/AGGG 5’ and 5’ GAAA/AAAG 5’ motifs:

These motifs are mainly present in centromeric satellite sequences and their purin content is asymmetrically distributed. These kind of motifs came in existence when one strand is rich in purine.