The Role of Water Structure in Conformational Changes of Nucleic Acids in Ambient and High Pressure Conditions

Jan Barciszewski 

Polish Academy of Sciences, Institute of Bioorganic Chemistry, Noskowskiego 12, PoznaƄ 61-704, Poland

Abstract


In the paper I will describe various data concerning the structure and
properties of water at normal conditions as well as at high salt
concentration and under high pressure. I will correlate the already
observed conformational changes of nucleic acids with changes in the
water structure and activity. The mechanism for this process which
accounts the changes in the water structure is suggested.
Oligodeoxyribonucleotides provide the best model for detailed
inspection and discussion of high pressure on DNA conformational
transitions, mainly because many crystallographic and spectroscopic
data are available at the same time. Results of high pressure
application experiments showed that this technique provides equivalent
or very similar effects as those observed at ambient conditions. It is
evident that the structure of water is strongly effected by high
pressure and the formation of octameric water from tetramers results
in smaller volume.
Many of those structures feature water molecules burried at the
intermolecular interface or assign them with reasonable confidence to
good geometry of water oxygen atoms at the coordination space of
hydrogen bond donors and acceptors. Thus, hydrogen bonding networks
between proteins and nucleic acids often include water molecules,
which have not been anticipated from our previous understanding of the
molecular basis for macromolecular recognition which predicted always
direct contacts between functional groups. Several basic questions
concerning water interactions with proteins and nucleic acids,
strength of these interactions, their localisation, structure and
effect on the conformation of various biological macromolecules are of
great importance. Water molecules appear to be both the cement that
fills crevices between amino acid building blocks and the lubricant
that allows motion of these elements. In consequence, they allow a
biological molecule to adopt a tertiary structure without being
trapped in local minimum, as well as compensate for a poor steric fit
of side chains in macromolecule interiors of substrates in the binding
sites. We provide data which supports the view that the main driving
force in the nucleic acids conformational changes under high pressure
is a new structure of water molecules, formation of which has negative
D V. Once the water changed its structure, it can induce different
foldings of the polynucleotide chain and open room for other
interactions, which stabilize e.g.the Z-DNA conformation. It has been
shown that specific interactions of the two lone pairs of 04' of
deoxyribose stabilizes the left-handed DNA conformation due to the
hyperconjugative effect within a cytidine nucleotide and between
cytosine residue and guanine base in d(CG) containing
oligonucleotides. Finally we conclude that specific water interactions
with nucleic acid backbones are the driving force for nucleic acids
conformational changes. Whether the newly induced conformation is
stable or not, depends on the specific nucleotide sequence, which may
provide additional electronic stabilizing effects. From various
biophysical, biochemical and crystallographical data we conclude that
the Z-DNA form can be induced only at low water activity effected by
high salt or high pressure and accompanied by the stabilizing
conjugative effect of the cytidine 04'electrons of the alternating CG
base pairs. Finally, we belive that the question of how water
interacts with the solute is more appropriate than the question of how
macromolecules interact with water.

 

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Presentation: oral at High Pressure School 1999 (3rd), by Jan Barciszewski
See On-line Journal of High Pressure School 1999 (3rd)

Submitted: 2003-02-16 17:33
Revised:   2009-06-08 12:55