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6. Angive andre konformationer i DNA end Watson-Crick dobbelthelix, fx. cruciform DNA, tre-strenget helix, fire-strenget DNA og slipped/mispaired DNA
Devlin, s.44-48, fig. 2.33
Stryer, s.747-750, fig. 27.4, 27.10
Stryer, s.750 table 27.1

 

There are several confirmations of double helical DNA. Depending on conditions and base sequence, the double helix can acquire various forms of distinct geometrics. 11 forms have been described. Thou, there are 3 main conformations:

B-DNA (the Watson-Crick DNA)

·                     base pairs are relatively perpendicular to the helix axis
·                     has a major and minor groove
·                     right-handed helix
·                     appears at high humidity and low salt concentration
·                     app. 10 base pairs per helical turn

 Most DNA is in B-from under physiological conditions.

A-DNA 

·                     the base pairs are tilted from the plane perpendicular 19˚ to the helix axis
·                     major and minor groove
·                     right handed helix
·                     appears at low humidity and high salt concentration
·                     shorter and thicker then B-DNA
·                     11 base pairs per helical turn  

Double stranded regions of RNA and some RNA-DNA hybrids adopt the form very similar to A-DNA.

Z-DNA

·                     left-handed helix
·                     zigzag backbone
·                     only one groove

 

Triple stranded DNA
Devlin, s.50-53, fig. 2.29; 2.30

Triple-stranded DNA can be formed by antiparallel binding of an oligonucleotide to the homopurine strand of a Watson-Crick double helix. Purines have two groups that can participate in additional base pairing:

Selective triplets can be formed between A and A-T pairs as well as G and G-C pairs. The new DNA molecule has 3 strands.  (fig.2.29)

Base stacking plays an important role in stabilizing the seqeunce, but because there are three negatively charged phosphate-sugar backbones, the repulsion between them is bigger leading to a less stable stucture. The structure can be stabilized by adding Mg++ - jons, that shields the negative phosphate charges.

Potential triple helices regions are especially common near sequences involving gene regulation.

Four-stranded DNA
 Devlin, s. 54-56, fig. 2.32; 2.33
 

Four-stranded DNA is made up by stacking of the so-called G-quartets.

G-quartet - tetrameric structures containing guanine nucleotides and highly G-rich polynucleotides. They can stack upon eachother and form a multylayered structure.

G-quartets are formed when 4 coplanar guanines of different G-rich polynucleotides form a tetrameric structure making Hoogstein hydrogen bonds. The cavity in the center of the quartet can accomodate Na+ og K+ jons, which interact with guanine oxigens (O-6) and stabilize the hole. 

The exsistance of four-stranded DNA in vivo has never been proved. A possible function can have something to do with telomeres that contain repetitive G-sequences - TTAGGG, fx. initiation and termination of replication and recombination.

In vitro experiments indicated that oligonucleotides with the appropriate seqeunce can form G-quartets in telomeres.

Cruciform DNA
 Devlin, s.49-50, fig. 2.28
 

Cruciform DNA is created as a result of inverted repeats. Inverted repeats are wide spread in the human genome. It has been speculated that they may function as molecular switches for replication and transcription.

An inverted repeat is a DNA sequence on one strand that has its complementary sequence on the same strand, just a little bit more down the sequence. If the complementary sequence is read in 5'-3' direction, it is exactly the same as the template.

Imagine a nucleotide sequence (which i will call the "template" sequence in the lack of a better word) that appears on one DNA strand and pairs with its complementary (progeny) sequence on the antiparallel strand. The same template sequence is found few nucleotides down on the antiparallel strand, just in the opposite direction and this one pairs with the complementary sequence on the first DNA strand. This means that we have the template and complementary sequence on the same strand, just divided by some nucleotides. Both the template and the complementary seqeunce lieing on the same strand have the same seqeunce of nucleotides if read in 5'-3' direction.

The reason why no symmetric inverted repeat is formed, is that there is fx. a uneven number of bases in the sequence, so there can be no symmetry, plus the seqeunce lies further down the molecule.

Disruption of hydrogen bonds between the complementary sequences and formation of intra-strand hydrogen bonds (between the template and complementary sequence on the same strand of DNA) on both helices creates a cruciform DNA.

The loops generated by cruciform formation require unpairing of 3-4 bases at the end of the hairpin. These were actually the bases that were in between the template and complementary sequence on the same strand.

The presence itself of invert repeats is favorable, but not enough to cause formation of cruciform DNA. The double helix DNA finds in thermodynamically unfavorable to create cruciform DNA. The DNA needs to be unwinded if the cruciform structures is to be formed. Unwinding favors the intra-strand hydrogen bonding.

No function of the cruciform DNA has been established. 

Slipped/mispaired DNA 
Devlin, s. 56-8, fig 2.35; fig. 2.36
 

It appears in DNA regions with direct repeat symmetry - presence of two adjacent tandem repeats. This means that the same template DNA sequences are found on one DNA strand right after each other.

 The formation of slipped DNA involves the unwinding of the double helix and realignment of the strands in that way that the first DNA template sequence pairs with the complementary sequence which was previously paired with the second template sequence or vice versa. Therefore, 2 isomeric forms can be made. 

This realignment generates two single-stranded loops, the second template strand and the first complementary strand in the example I gave. It is vice versa with the isomeric for.

Slipped DNA is involved in spontaneous frame shift mutagenesis, when 1 base is slipped. Depending if the base has been slipped in the complementary or template strand, it can manifest as addition or deletition of the base.

A deletition of addition of a longer segment during DNA replication can be seen due to larger sequences of slipped DNA. (fig. 2.36)

 

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