III SIMPÓSIO INTERDISCIPLINAR FÍSICA +
BIOINFORMÁTICA
22 A 25 DE ABRIL DE 2014
UNIVERSIDADE FEDERAL DE UBERLÂNDIA, UBERLÂNDIA, MINAS GERAIS
Determination of DNA mesoscopic model parameters for Inosine
*Rodolfo Vieira Maximiano¹ (PG), Gerald Weber¹ (PQ)
¹Universidade Federal de Minas Gerais.
*rodolfomaxi@gmail.com.
Keywords: Peyrard-Bishop model, Deoxyinosine, DNA mesoscopic model.
INTRODUCTION
Deoxyinosine, or inosine in short, is a naturally
occurring base which is used for several
biotechnological applications. It is thought that
inosine (I) pairs to all four bases (A,T,G and C)
indiscriminately, a property which makes it attractive
for the design of sequencing probes and PCR
primers [1,2]. This thermodynamic neutrality of
inosine is essential for its use as an "universal"
base. However, over the past few years it has
emerged that inosine may not be so universal after
all.
A
comprehensive
overview
of
its
thermodynamics properties is needed and is largely
missing in literature. In particular, there is currently
an incomplete knowledge of the hydrogen bonds of
the inosine base pairs coming from only one NMR
study [3].Here we perform calculations to obtain the
values for the hydrogen bonds strength and elastic
constants related to inosine.
METHODS
The method consists in calculating the predicted
melting temperature by varying the strength of the
hydrogen bonds and stacking parameters. We
perform such calculations to obtain the values for
the hydrogen bonds strength and elastic constants
related to inosine. We used an experimental melting
database that contains all possible nearestneighbours combinations for inosine[1], with a twostep procedure to minimize the difference between
expected and experimental temperatures.
CONCLUSIONS
The average openings correlate perfectly with the
reported thermodynamic stability trends. We show
that
the
thermodynamic
stability
trend
I.C> I.A > I.T ≈ I.G> I.I reported in earlier
works only holds for the particular sequences that
were studied at the time. In fact, we show that no
such general trend does exist for inosine and that its
thermodynamic stability is strongly context
dependent, that is, that inosine is not truly a
universal base. However, we were able to work out
the subset of inosine nearest-neighbours where this
neutrality can still be maintained and be used for the
intended biotechnological applications.
RESULTS AND DISCUSSION
We were able to work out all relevant PeyrardBishop parameters for inosine. In particular, we
obtained the first complete overview of Morse
potential (which represents hydrogen bonds) for it.
From these parameters we are able to calculate the
average openings of the double helix as function of
temperature. These average openings correlate
perfectly
with
the
previously
reported
thermodynamic stability trends, as shown on Fig1.
Figure 1. Average Opening of the sequence found in
[2].
2
ACKNOWLEDGMENTS
The authors would like to thank CNPq, Capes,
Fapemig and National Institute for Complex Systems
for funding.
_________________________
[1] N. E. Watkins Jr and J. Santalucia Jr. Nucleic Acids Res., 33, 19,
6258 (2005).
[2] F. H. Martin, M. M. Castro, F. Aboul-ela, I. Tinoco Jr, Nucleic Acids
Res., 13, 24, 8927 (1985).
[3] E. M. B. Janke, F. Riechert-Krause, K. Weisz, J. Phys. Chem. B, 115,
8569 (2011).