|
Stability analysis of r(5'-GGCC-3')2 vs. r(5'-iGiGiCiC-3')2
 Isoguanosine (iG) and isocytidine
(iC) are unnatural nucleotides that have some interesting properties (Yildirim
and Turner, 2005). They form an unnatural base pair, iG-iC, in which the
amino and carbonyl groups of G and C are transposed to create iG and iC
(Switzer et al., 1993). Experimentally, it is shown that the stability of
r(5'-iGiGiCiC-3')2 is more favorable than r(5'-GGCC-3')2
(Chen et al., 2001; Xia et al., 1998). Even though iG-iC and G-C pairs are
isosteric, the electron densities are different.
|
|
ΔG37
(kcal/mol) |
Tm
(˚C) |
|
r(5'-GGCC-3')2 |
5.37 |
34.3 |
|
r(5'-iGiGiCiC-3')2 |
7.17 |
47.5 |
Theoretical and computational
explanation to this phenomenon is not given, yet. We follow the
Thermodynamic Integration (TI) Approach of AMBER package (of molecular
simulation programs) to describe this phenomenon.
Theoretical
Work:
In TI Approach, a hybrid
Hamiltonian (which is a mix of initial and final states) is described as
follows:
where E(λ) is the hybrid
Hamiltonian, E0 and E1 are the Hamiltonians of the
initial and final states, respectively, and f(λ) is the mixing function
defined with a mixing parameter λ.
We have changed the source code of
‘sander’ to use a new mixing function, which enables us the use of dummy
atoms in both initial and final states (http://amber.scripps.edu/doc9/amber9.pdf).
The old mixing rule has
the following mixing function:
We have implemented a new
mixing rule to sander, which uses the following mixing function:
The mixing parameter λ is a real
number, which has to satisfy 0 < λ < 1. ‘k’ is a positive
integer.
Computational
Work:
The Thermodynamic Cycle
for this system can be described as follows:
ΔG1 and ΔG3
are experimentally known. TI Approach is applied for both helical and
single stand simulations to end up with ΔG2 and ΔG4.
Special attention should be given
to the single strand simulation because of the random coil form of the
structures. Conformational analysis of single-stranded RNA 5’GGCC3’ is
done to get structures that will be good enough to describe the single
strand simulations.
Do
single-stranded RNA structures have some preferred conformations?
It is believed that
single-stranded RNA structures have random coil forms, which means there
are no preferred (stable) conformations. Some single-stranded RNA
structures are reported to have a preferred conformation (Doornbos et al.,
1983), especially adenine rich single-stranded RNA structures (Isaksson
et al., 2004). Computational work on single-stranded RNA structures is
done to see if they retain any stable structure.
Structural preferences of 2X2 Tandem GA pairs:
Depending on the closing base
pairs, 2X2 Tandem GA pairs can have different conformational preferences.
GA pairs in r(5’GGAC3’)2 have imino hydrogen bonded mismatches,
while GA pairs in r(5’CGAG3’)2 have sheared GA mismatches (Wu
and Turner, 1996; SantaLucia and Turner, 1993). This kind of structural
preference is again seen in 2X2 Tandem GA pairs when they are closed by
iGiC base pairs (Chen et al., 2007). Computational and theoretical work is
going to be done on these projects.
----------------- References
----------------------------------------------------------------------------------------------------------
“RNA challenges for computational
chemists” I. Yildirim and D. H. Turner, Biochemistry, 44, 13225-13234
(2005).
“Enzymatic recognition of the
base-pair between isocytidine and isoguanosine” C. Y. Switzer, S. E.
Moroney, and S. A. Benner, Biochemistry, 32, 10489-10496 (1993).
“Stability and Structure of RNA
Duplexes Containing Isoguanosine and Isocytidine,” X. Chen, R. Kierzek,
and D. H. Turner, J. Am. Chem. Soc., 123, 1267-1274 (2001).
“Thermodynamic Parameters for an
Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with
Watson-Crick Base Pairs,” T. Xia, J. SantaLucia, Jr., M. E. Burkard, R.
Kierzek, S. J. Schroeder, X. Jiao, C. Cox, and D. H. Turner, Biochemistry,
37, 14719-14735 (1998).
“Conformational analysis of the
single-stranded ribonucleic acid A-A-C-C. A one-dimensional and
two-dimensional proton NMR study at 500 MHz.” J. Doornbos, C. T. Wreesmann,
J. H. Van Boom, and C. Altona, European Journal of Biochemistry, 131,
571-579 (1983).
“Single-stranded adenine-rich DNA
and RNA retain structural characteristics of their respective
double-stranded conformations and show directional differences in stacking
pattern” J. Isaksson, S. Acharya, J. Barman, P. Cheruku, and J.
Chattopadhyaya, Biochemistry, 51, 15996-16010 (2004).
“Solution Structure of
(rGCGGACGC)2by Two-Dimensional NMR and the Interative Relaxation Matrix
Approach,” M. Wu and D. H. Turner, Biochemistry, 35, 9677-9689 (1996).
“Structure of (rGGCGAGCC)2in
Solution from NMR and Restrained Molecular Dynamics,” J. SantaLucia, Jr.
and D. H. Turner, Biochemistry, 32, 12612-12623 (1993).
“Stacking Effects on Local
Structure in RNA: The Structure of Tandem GA Pairs Changes When Flanking
GC Pairs are Replaced by isoG-isoC Pairs” G. Chen, R. Kierzek, I. Yildirim,
T. R. Krugh, D. H. Turner, and S. D. Kennedy, J. Phys. Chem., accepted
(2007). |
