Synthesis, base pairing and structure studies of geranylated RNA

Article abstract of DOI:10.1093/nar/gkw544

Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium. The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNA^Glu_UUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon-anticodon interaction during ribosome binding.

Full text of DOI:10.1093/nar/gkw544

Nucleic Acids Research Advance Access published June 15, 2016
Nucleic Acids Research, 2016
1
doi: 10.1093/nar/gkw544
Synthesis, base pairing and structure studies of
geranylated RNA
Rui Wang1,2,†, Sweta Vangaveti2,†, Srivathsan V. Ranganathan2, Maria Basanta-Sanchez2,
Phensinee Haruehanroengra1,2, Alan Chen1,2 and Jia Sheng1,2,*
1Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA and 2The RNA
Institute, University at Albany, State University of New York, Albany, NY 12222, USA
Received February 18, 2016; Revised May 30, 2016; Accepted June 2, 2016
ABSTRACT
and non-coding RNA of all three primary phylogenetic do-
mains (Archaea, Bacteria and Eukarya) (1,2). These modifi-
cations have been increasingly demonstrated to play critical
roles in many biological processes and be highly involved
in many human diseases (3–6). Additionally, it is believed
that these chemical modifications are few of the most evo-
lutionarily conserved properties in RNAs, and some of the
modified nucleobases are relics of the RNA World, where
they may have enhanced the chemical diversity of RNA
prior to the emergence of proteins (7). Therefore, studying
the structures and functions, such as base pairing specificity
and enzymatic recognition properties of these RNA chemi-
cal modifications, will be significant for further elucidation
of RNA functions as both genetic information carriers and
biological catalysts, the development of new RNA-targeted
therapeutics, as well as origin of life studies.
tRNAs contain over 90 different chemical modifica-
tions that play central regulatory roles in codon–anticodon
recognition, tRNA charging with specific amino acids and
peptide synthesis during translation (8–16). Uracil is the
most modified nucleobase and among the nearly 60 known
uridine modifications, more than 15 contain C2 thiolation,
which is known as 2-thiouridine and its C5 derivatives (1).
The 2-thiouridine geranylation, in which a large hydropho-
bic geranyl group is covalently linked to the sulphur atom
of the 2-thiouridine derivatives (as shown in Figure 1, com-
pound 3, 4, 5), has been discovered very recently as a new
natural RNA modification in several bacteria including Es-
cherichia coli, Enterobacter aerogenes, Pseudomonas aerug-
inosa and Salmonella Typhimurium, at a frequency of up
to 6.7% (∼400 geranylated nucleotides per cell) (17). These
modified residues are located in the first anticodon posi-
tion (position 34) of tRNAs specific for lysine, glutamine
and glutamic acid. The enzyme SelU, the selenouridine
synthase that is known to transfer the 2-thiouridine to 2-
selenouridine, another natural RNA analog, is also respon-
sible for the biosynthesis of these geranylated nucleosides
(Scheme 1) (18–20). This suggests that the RNA geranyla-
tion might also play regulatory roles in the selenonucleo-
Natural RNAs utilize extensive chemical modifica-
tions to diversify their structures and functions. 2-
Thiouridine geranylation is a special hydrophobic
tRNA modification that has been discovered very
recently in several bacteria, such as Escherichia
coli, Enterobacter aerogenes, Pseudomonas aerugi-
nosa and Salmonella Typhimurium. The geranylated
residues are located in the first anticodon position
of tRNAs specific for lysine, glutamine and glutamic
acid. This big hydrophobic terpene functional group
affects the codon recognition patterns and reduces
frameshifting errors during translation. We aimed
to systematically study the structure, function and
biosynthesis mechanism of this geranylation path-
way, as well as answer the question of why nature
uses such a hydrophobic modification in hydrophilic
RNA systems. Recently, we have synthesized the
deoxy-analog of S-geranyluridine and showed the
geranylated T-G pair is much stronger than the ger-
anylated T-A pair and other mismatched pairs in
the B-form DNA duplex context, which is consistent
with the observation that the geranylated tRNAGlu
UUC
recognizes GAG more efficiently than GAA. In this
manuscript we report the synthesis and base pair-
ing specificity studies of geranylated RNA oligos. We
also report extensive molecular simulation studies to
explore the structural features of the geranyl group
in the context of A-form RNA and its effect on codon–
anticodon interaction during ribosome binding.
INTRODUCTION
Natural RNA systems utilize a variety of chemical modifi-
cations to achieve structural and functional specificity and
diversity. Currently, there are over 150 natural modifica-
tions that have been discovered in mRNA, rRNA, tRNA
*To whom correspondence should be addressed. Tel: +1 518 437 4419; Fax: +1 518 442 3462; Email: jsheng@albany.edu
†These authors contributed equally to the paper as first authors.
ꢀ
C
The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which
permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
journals.permissions@oup.com

2 Nucleic Acids Research, 2016
Figure 1. Chemical structures of uridine (U, 1), 2-thiouridine (s2U, 2), geranylated 2-thiouridine (ges2U, 3), geranylated 5-methylaminomethyl-2-
thiouridine (mnm5ges2U, 4) and geranylated 5-carboxylmethylaminomethyl-2-thiouridine (cmnm5ges2U, 5).
Scheme 1. The selenouridine synthase (SelU) has dual functions: (A) to install a geranyl group to the sulphur atom in the presence of geranyl pyrophosphate;
and (B) to replace sulphur with selenium in the presence of selenophosphate. The R group represents the mnm- or cmnm- in position 5 of compound 4
and 5 in Figure 1.
side biosynthesis, an important biosynthetic pathway in live
cells (21,22). Although the geranylated 2-thiouridine might
merely be the intermediate product in the transformation
of 2-thiouridine to 2-selenouridine (23,24), the question of
why nature uses such a bulky hydrophobic group (the only
terpene functionality discovered so far) in hydrophilic RNA
systems remains unresolved. From an evolutionary point of
view, it is quite reasonable to speculate that such hydropho-
bic terpene groups might be chemical relics from ancient
RNA-mediated lipid synthesis (25).
DNA duplex context. Our findings are consistent with the
observation that the geranylated tRNAGlu
recognizes
UUC
GAG more efficiently than GAA in previous studies (26).
In this manuscript, we present the synthesis and base pair-
ing specificity studies of geranylated RNA oligos, as well as
extensive molecular simulation studies to explore the struc-
tural features of the geranyl group in A-form RNA duplex
in comparison with B-form DNA, and its effect on codon–
anticodon interaction during ribosome binding.
This hydrophobic geranyl group has been demonstrated
to affect the codon recognition and decrease the frameshift-
ing errors during translation (17). In our studies, we
have synthesized the deoxy-analog of S-geranyluridine and
showed the geranylated T-G pair is much stronger than ger-
anylated T-A and other mismatched pairs in the B-form
MATERIALS AND METHODS
Synthesis of 2-thio-geranyluridine phosphoramidite
1-((2R,3R,4R,5R)-5-((bis(4-
methoxyphenyl)(phenyl)methoxy)methyl)-3-((tert-
butyldimethylsilyl)oxy)-4-hydroxytetrahydrofuran-2-yl)-

Nucleic Acids Research, 2016 3
2-(((E)-3,7-dimethylocta-2,6-dien-1-yl)thio)pyrimidin-
4(1H)-one (8). The synthesis of compound 7 in Scheme 2
are presented in the Supplementray Data. A solution of 7
(573 mg, 1 mmol), geranyl bromide (0.6 ml, 3 mmol) and
N,N-diisopropylethylamine (0.53 ml, 3 mmol) in MeOH
(10 ml) was stirred at 25◦C for 12 h. The resulting reaction
mixture was quenched with water (10 ml), washed with
brine (8 × 30 ml) and dried over Na2SO4. The crude
product was concentrated in vacuo and directly subjected
to silica gel chromatography. A sticky liquid (651 mg, 92%
yield) was obtained after column flash chromatography,
␦ 147.52, 147.28; HRMS (ESI-TOF): molecular formula,
C55H77N4O8PSSi; [M+H]+: 1013.3993 (calc. 1013.3461).
Synthesis of RNA oligonucleotides
The oligonucleotides were chemically synthesized at 1.0
␮mol scales by solid phase synthesis using a MerMade
MM8 synthesizer. The geranyl uridine phosphoramidite
was dissolved in dichloromethane to a concentration of
0.07 M. I2 (0.02 M) in THF/Py/H2O solution was used
as an oxidizing reagent. Coupling was carried out using
5-ethylthio-1H-tetrazole solution (0.25 M) in acetonitrile
for 6-min, for both native and modified phosphoramidites.
About 3% trichloroacetic acid in methylene chloride was
used for the 5ꢁ-detritylation. Synthesis was performed on
control-pore glass (CPG-500) immobilized with the appro-
priate nucleoside through a succinate linker. All the reagents
used are standard solutions obtained from ChemGenes
Corporation. The oligonucleotide was prepared in DMTr-
off form. After synthesis, the oligos were cleaved from the
solid support and fully deprotected with concentrated am-
monium solution at room temperature for 14 h. The solu-
tion was evaporated to dryness by Speed-Vac concentrator
and was desilylated using a triethylamine trihydrogen fluo-
ride (Et3N•3HF) solution at 65◦C for 2.5 h. The reaction
was quenched with 1 ml of water and the RNA was precip-
itated by adding 0.2 ml of 3 M sodium acetate and 6 ml of
n-butanol. The solution was cooled to −80◦C for 1 h before
the RNA was recovered by centrifugation and finally dried
under vacuum.
1
TLC Rf = 0.4 (1% MeOH in CH2Cl2). H nuclear mag-
netic resonance (NMR) (400 MHz, CD3OD) ␦ 7.77 (d, J =
8.0 Hz, 1H, H-6), 7.46 (d, J = 6.8 Hz, 2H), 7.37 (d, J = 4.4
Hz, 2H), 7.30 (d, J = 8.4 Hz, 2H), 7.22-7.09 (m, 4H), 6.19
(d, J = 7.6 Hz, 1H), 5.83 (d, J = 8.0 Hz, 1H), 5.42 (t, J =
7.6 Hz, 1H), 5.02 (d, J = 5.6 Hz, 1H), 4.27-4.24 (m, 1H),
4.06 (br s, 1H), 3.99-3.92 (m, 2H), 3.82 (d, J = 8.4 Hz, 1H),
3.76 (s, 3H), 3.75 (s, 3H), 3.64 (d, J = 11.6 Hz, 1H), 3.42
(d, J = 4.4 Hz, 1H), 1.96 (br s, 4H), 1.72 (s, 3H), 1.63 (s,
3H), 1.49 (s, 3H), 0.81 (s, 9 H), 0.05 (s, 3H), 0.01 (s, 3H);
13C NMR (100 MHz, CD3OD) ␦ 169.98, 164.37, 158.99,
158.83, 144.83, 142.05, 140.09, 135.25, 135.05, 130.19,
129.88, 128.93, 127.73, 127.63, 127.37, 127.02, 126.53,
126.28, 123.39, 116.84, 112.74, 112.33, 108.37, 90.72, 87.69,
77.43, 71.20, 63.83, 54.19, 54.18, 54.15, 40.64, 31.33, 27.38,
26.42, 25.89, 19.30, 17.78, 16.69, −5.32, −5.44; HRMS
(ESI-TOF): molecular formula, C46H60N2O7SSi; [M+H]+:
814.3970 (calc. 814.1283).
3-((((2R,3R,4R,5R)-2-((bis(4-methoxyphen-
yl)(phenyl)
methoxy)methyl)-4-((tert-butyldimethylsil-
yl)oxy)-5-(2-(((E)-3,7-dimethyl-octa-2,6-dien-1-yl)thio)-
4-oxopyrimidin-1(4H)yl)tetrahydrofuran-3-yl)oxy)-
HPLC analysis and purification
(diisopropylamino)phosphino)propanenitrile
(9).
To
RNA oligonucleotides were purified by ion-exchange
HPLC using a PA-100 column from Dionex at a flow
rate of 1 ml/min. Buffer A was pure water, and buffer
B contained 2M ammonium acetate (pH 7.1). The RNA
oligonucleotides were eluted with a linear gradient of 0–
50% buffer B over 20 min. The collected fractions were
lyophilized, desalted with Waters Sep-Pac C18 columns and
re-concentrated.
a solution of compound 8 (200 mg, 0.31 mmol) in
CH2Cl2 (5.0 ml), DIPEA (0.22 ml, 0.62 mmol) was
added at 0◦C under Ar atmosphere. 2-Cyanoethyl N,N-
diisopropylchlorophosphoramidite (0.14 ml, 0.12 mmol)
was carefully injected to this mixture over 15 min at 0◦C.
The reaction was warmed to ambient temperature for 5 h
before being quenched with sodium bicarbonate solution.
The solvent was extracted with CH2Cl2 and the organic
layer was evaporated. Flash column chromatography
was used for purification, TLC Rf = 0.4 (1% MeOH in
Enzymatic hydrolysis and UHPLC–MS/MS analysis of
geranyl–RNA oligo
1
CH2Cl2), to yield 9 as a white sticky solid. H NMR (400
Major RNA nucleoside standards were purchased (Sigma-
Aldrich Co). Isotopically labeled guanosine [13C][15N]G
used as the internal standard (IS) was a gift from Cambridge
Isotope Laboratories, Inc. Prior to UHPLC-MS/MS anal-
ysis, 1.0 pg/␮l [13C][15N]-G was added, as IS, to 100 ng of
total RNA to be hydrolyzed to the composite mononucle-
osides via a two-step enzymatic hydrolysis. The first step of
phosphodiester bond cleavage was accomplished with nu-
clease P1, resulting in nucleoside-5ꢁ-monophosphates. Op-
timum nuclease P1 activity was achieved at pH 5.5 by the
addition of 1/10 of the volume of 1.0 M ammonium ac-
etate at pH 5.5. For each 0.5 absorbance unit of RNA, two
units of nuclease P1 were added and incubated overnight at
37◦C. The second step of nucleoside preparation uses bacte-
rial alkaline phosphatase (BAP) to cleave the 5ꢁ-phosphate
from the nucleosides resulting in individual nucleosides and
MHz, CD3OD) ␦ 7.69 (d, J = 8.4 Hz, 1H, H-6), 7.43-7.21
(m, 10 H, H-Ar), 6.79 (d, J = 8.4 Hz, 2H, H-Ar), 6.72 (d,
J = 8.4 Hz, 2H, H-Ar), 6.20 (d, J = 7.6 Hz, 1H), 5.80 (d,
J = 7.6 Hz, 1H), 5.41 (d, J = 8.4 Hz, 1H), 5.02 (d, J =
8.0 Hz, 1H), 4.60 (s, 2H), 4.46–4.42 (m, 1H), 4.41 (s, 1H),
4.05–3.90 (m, 4H), 3.78 (s, 3H), 3.76 (s, 3H), 2.72 (dd, J =
12.0, 6.4, Hz, 2H), 2.15 (s, 6H), 1.95 (s, 4H), 1.72 (s, 3H),
1.64 (s, 3H), 1.50 (s, 3H), 1.29 (s, 4H), 1.21 (t, J = 6.4 Hz,
12H), 0.83 (s, 9H, H-tBu), 0.06 (s, 3H, H-Me), 0.03 (s, 3H,
H-Me); 13C NMR (100 MHz, CD3OD) ␦ 164.35, 158.99,
158.86, 144.82, 142.06, 136.23, 136.12, 134.76, 130.55,
130.20, 128.04, 127.36, 126.61, 123.45, 116.77, 112.78,
108.42, 101.91, 90.45, 63.89, 58.57, 54.16, 43.01, 42.88,
29.86, 25.90, 24.99, 24.40, 23.58, 23.49, 19.59, 19.52, 17.85,
16.31, 15.22, −6.74, −6.94; 31P NMR (162 MHz, CD3OD)

4 Nucleic Acids Research, 2016
Scheme 2. Synthesis of S-2-thiouridine phosphoramidite 9. Reagents and conditions: (a) TMSCl, HMDS; (b) 2,3,5-tri-O-benzoyl-␤-D-ribofuranose,
SnCl4, 1,2-dichloroethane; (c) NaOMe, MeOH; (d) Di-tert-butylsilyl ditriflate; TBDMS-Cl, Imidazole, DMF; (e) HF•Py, Py; (f) DMTrCl, Py; (g) ger-
anyl bromide, DIPEA, MeOH; (h) (i-Pr2N)2P(Cl)OCH2CH2CN, (i-Pr)2NEt, CH2Cl2.
phosphoric acid. For optimum BAP activity, the pH was
adjusted to pH 8.3 by adding 1/10 of the volume of 1.0
M ammonium bicarbonate pH 8.3. One unit of BAP was
added for each 0.5 absorbance units of RNA and incubated
at 37◦C for 2 h. The nucleoside products were lyophilized
and stored at −20◦C. Samples were reconstituted in 0.01%
formic acid in RNAse-free water to a final concentration of
1 ng/␮l prior to UHPLC-MS/MS analysis. A negative con-
trol sample was included in the dataset. The control com-
prised of the enzymes, IS and reagents used during the en-
zymatic hydrolysis.
containing 0.01% formic acid (Buffer A) and 50% acetoni-
trile in aqueous 0.01% formic acid pH 3.5 (Buffer B). Tan-
dem MS analysis of DNA nucleosides was performed on a
Waters XEVO TQ-STM (Waters, USA) triple quadrupole
mass spectrometer equipped with an electrospray ionization
(ESI) source maintained at 150◦C with the capillary voltage
set at 1kV. The desolvation gas, nitrogen, was maintained at
500 l/h and the desolvation temperature was set at 500◦C.
The cone gas flow and nebulizer pressure were set to 150
l/h and seven bars, respectively. Composition analysis was
performed in ESI positive-ion mode using multiple-reaction
monitoring (MRM). All of the commercial and synthesized
nucleoside standards were characterized individually by di-
rect infusion MS. The ion transitions, cone voltage and col-
lision energy used for UHPLC-MS/MS were determined
using MassLynx V4.1Intellistart software. Retention times
and the corresponding protonated molecular and product
ion pairs [MH+/BH2+] were obtained for each individual
nucleoside.
Hydrolyzed oligos were subjected to chromatography us-
ing a Waters ACQUITY I-Class UPLCTM (Waters, USA)
liquid chromatographic system equipped with a binary
pump and autosampler that was maintained at 4◦C. A Wa-
ters ACQUITY UPLCTM HSS T3 column (2.1 × 50 mm
1.7 ␮m) and a HSS T3 guard column (2.1 × 5 mm, 1.8 ␮m)
were used for the separation. The assay was completed at a
flow rate of 0.2 ml/min and column temperature of 25◦C.
Mobile phases included RNase-free water (18.0 Mꢀcm−1
)

Nucleic Acids Research, 2016 5
UV and circular dichroism (CD) spectroscopy
The system was subjected to energy minimization to pre-
vent any overlap of atoms, followed by a 10 ns equilibration
MD run. 10 parallel simulations with the same equilibrated
starting conformations but with different starting velocities
were performed for 100 ns each, totaling 1 ␮s of production
run for each DNA/RNA duplex. Coordinates were stored
every picosecond for further analysis.
UV-Vis absorption spectra were measured on a Perkin-
Elmer Lambda 900 UV-Vis spectrometer. Methanol was
used as the solvent to dissolve the nucleoside. Circular
dichroism (CD) spectra were recorded with 5 ␮M RNA du-
plexes in 20 mM phosphate buffer (pH 7.0) on a JASCO-
815 spectropolarimeter at 20◦C over a wavelength range of
200–320 nm using a 1 cm path length quartz cuvette with a
scanning speed of 100 nm/min, bandwidth of 1.0 nm and
D. I. T of 1.0 s. Each spectrum was averaged from an accu-
mulation of four scans and baseline-corrected against the
buffer.
Ribosome. To study the effects of ges2U modification on
codon–anticodon interactions, two crystal structures of 16S
ribosomal subunit of Thermus thermophilus containing the
anticodon stem loop (ASL) of tRNALys and the mRNA
codon fragment in the decoding center, were obtained from
the protein data bank (PDB ID: 1XMO, 1XMQ). The two
structures differ in their codon sequences (1XMO has AAG
while 1XMQ has AAA as the codon). In order to investigate
the effects of modification, simulations were set up for each
codon–anticodon pair, with and without the ges2U modifi-
cation at position 34 of the ASL of tRNALys. To further in-
clude the effects of the naturally occurring modifications at
the position 5 of the base, the methyl-amino-methyl (mnm)
modified 2-thiouridine was used to mutate corresponding
U34. The missing atoms in the ribosome-associated pro-
teins were fixed using MOE (32). The simulation system
included the ribosomal subunit with all its associated pro-
teins, the ASL of the tRNA and the mRNA codon fragment
in a solution of 1 M KCl in a 3D periodic box. The box size
was 26 × 26 × 26 nm3, containing ∼11 800 K+ ions, ∼10 700
Cl− ions and roughly 539 600 water molecules (1.6 × 106
atoms). The system was subjected to energy minimization
to prevent any overlap of atoms, followed by a 1 ns equili-
bration and 5 ns production MD run. Coordinates of the
RNA components (rRNA, tRNA, mRNA) of the system
were stored every 1 ps for further analysis. A schematic of
the simulation set up is illustrated in Supplementary Figure
S23.
All MD simulations were performed using Gromacs-
4.6.3 package (33). The MD simulations incorporated leap-
frog algorithm with a 2 fs time-step to integrate the equa-
tions of motion. The system was maintained at 300 K,
using the velocity rescaling thermostat (34). The pressure
was maintained at 1 atm using the Berendsen (35) and
Parrinello-Rahman barostat (36) for equilibration and pro-
duction runs, respectively. The long-ranged electrostatic
interactions were calculated using particle mesh Ewald
(PME) (37) algorithm with a real space cut-off of 1.2 nm.
LJ interactions were also truncated at 1.2 nm. TIP3P model
was used represent the water molecules, and LINCS (38)
algorithm was used to constrain the motion of hydrogen
atoms bonded to heavy atoms.
Thermodenaturation of the RNA duplexes
Solutions of the duplex RNAs (1 ␮M) were prepared by dis-
solving the purified RNAs in sodium phosphate (10 mM,
pH 6.5) buffer containing 100 mM NaCl. The solutions
were heated to 85◦C for 3 min, then cooled slowly to room
temperature and stored at 4◦C overnight before melting
temperature (Tm) measurements. Prior to thermal denatu-
ration, the geranyl RNA duplex was bubbled under argon
for 5 min. Data points for each denaturizing curves were ac-
quired at 260 nm by heating and cooling from 5 to 85◦C four
times at a rate of 0.5◦C/min, using Cary-300 UV-Visible
spectrometer equipped with a temperature controller sys-
tem. The block temperature was used as the standard. The
thermodynamic parameters of each duplex strand were ob-
tained by fitting the melting curves in the Meltwin software
(27).
Simulation methods
DNA/RNA duplexes. To study the ges2U modification in
the context of the duplex using molecular dynamics (MD)
simulations, we developed AMBER (28) type force-field pa-
rameters for the atoms of the modified nucleoside. For ob-
taining the partial charges on the atoms, we used the on-
line RESP charge-fitting server, REDS (29). The geome-
try of the modified nucleoside was energy minimized, and
Hartree-Fock level theory and 6–31G* basis-sets were em-
ployed to arrive at a set of partial charges (30). AMBER-
99 force-field parameters were used for bonded interactions
(28), and AMBER-99 parameters with Chen-Garcia cor-
rections were used for LJ interactions (31). The unmodified
RNA and DNA duplexes were constructed using nucleic
acid builder suite of AMBER 11 package. The sequence
of the RNA duplex is 5ꢁ-GGACUXCUGCAG-3ꢁ and 3ꢁ-
CCUGAYGACGUC-5ꢁ, consistent with the experimental
work presented here. X and Y correspond to U/ges2U
and A/G, respectively. The DNA duplex sequence is 5ꢁ-
CTTCTXGTCCG-3ꢁ and 3ꢁ GAAGAYCAGGC-5ꢁ, consis-
tent with our previous work (26). X and Y are the DNA
counterparts of the above mentioned RNA nucleotides. Us-
ing the WebMO graphical editor, we performed mutations
such as, U to ges2U, T to ges2T and A to G, to get the dif-
ferent RNA and DNA duplexes for MD simulation studies.
The simulation system included the DNA or RNA duplex
in a solution of 1M NaCl solution in a 3D periodic box.
The box size was 6 × 6 × 6 nm3, containing the duplex, 152
Na+ ions, 130 Cl− ions and roughly 6600 water molecules.
RESULTS AND DISCUSSION
Synthesis of geranyl-2-thiouridine phosphoramidite and
geranyl–RNA oligonucleotide
We started the synthesis of 2-thiouridine (4, Scheme 2)
through regular Vorbru¨ggen glycosylation of the protected
ribofuranose with silylated 2-thiouracil (2) in the pres-
ence of Tin (IV) chloride, followed by the deprotection of
the benzoyl groups using base treatment. The simultane-
ous silylation of 3ꢁ and 5ꢁ-hydroxyl groups with Di-tert-

6 Nucleic Acids Research, 2016
butylsilyl (DTBS) ditriflate followed by the 2ꢁ-protection
with tert-butyldimethylsilyl (TBDMS) group gave the sily-
lated 2-thiouridine compound 5. Compound 5 was then se-
lectively desilyated with hydrogen fluoride in pyridine and
tritylated with trityl chloride at the 5ꢁ position to gener-
ate the key intermediate 7 with satisfying yield. The ger-
anyl group was installed to the 2-sulfur center before the fi-
nal phosphoramidite building block 9 was synthesized. It is
noteworthy that the geranyl-2-thiouridine nucleoside, which
is the 2-thio-geranylated product of compound 4, shows a
UV absorption peak at 240 nm, compared to the 260 nm
for native uridine (Supplementary Figure S24). We have
demonstrated previously that this S-2-thio-geranyl group
is well compatible with the solid phase synthesis condi-
tions by using dichloromethane as the solvent. In order to
test its stability under fluoride treatment, which is neces-
sary for regular RNA deprotection and purification pro-
cess, we treated the S-2-geranyl-thiouridine nucleoside with
Et3N•3HF/Et3N at 65◦C for 4 h. No decomposed prod-
uct was detected. After we applied the phosphoramidite to
the solid phase synthesizer and made the geranylated RNA
oligonucleotide, the ESI-MS of the purified RNA showed
the correct mass with the presence of the geranyl group
(Supplementary Figure S25).
anylated RNA duplexes, 5ꢁ-GGACUXCUGCAG-3ꢁ and
3ꢁ-CCUGAYGACGUC-5ꢁ, with Watson–Crick and other
non-canonical base pairs (X pairs with Y) are shown in Sup-
plementary Figure S27A and B. Their detailed temperature
data are summarized in Table 1. Compared to our previous
DNA duplex results, this hydrophobic geranyl group in the
Watson–Crick face of RNA duplex has stronger effects on
decreasing the overall stability of duplexes containing both
native and non-canonical base pairs. As indicated in Ta-
ble 1, one single geranylation decreases the Tm by 26.2◦C,
corresponding to a ꢁG0 reduction of 11.0 kcal/mol, for
the native duplex (entry 1versus 5). The Tm drops 13.3◦C
for the U-G mismatch containing duplex after geranylation
(entry 2 versus 6), 13.7◦C for the U-C mismatch one (en-
try 3 versus 7) and 14.3◦C for the U-U mismatch one (en-
try 4 versus 8), corresponding to a ꢁG0 reduction of 6.7,
4.4 and 5.5 kcal/mol, respectively. When directly compar-
ing the Watson–Crick base pairs (U-A and ges2U-A) with
their own other mismatched pairs, as shown in the ꢁTm col-
umn, it is clear that the geranyl-2-thiouridine has a stronger
pairing preference for G compared to other bases. The Tm
of duplexes containing ges2U-G pair is 10◦C higher than
the native ges2U-A duplex, with an increased ꢁG0 of 2.6
kcal/mol (entry 5 and 6). Both the ges2U-C and ges2U-U
duplexes have very similar Tm as the ges2U-A one. In com-
parison, the native duplexes with U-G and U-A pairs have
similar stability and are much stronger than U-C and U-U
paired ones, with a slightly lower Tm (2.9◦C, entry 1 and 2)
in the U-G duplex. In this sense, the introduction of geranyl
group could increase the base pair specificity by stabilizing
the ges2U-G pair.
UHPLC-MS/MS analysis of geranyl nucleoside in RNA
oligo
In order to further confirm the incorporation and po-
sitions of geranyl modification in RNA oligonucleotide,
we hydrolyzed the geranyl strand and its native counter-
part to mononucleosides via nuclease P1 and BAP treat-
ment. The resultant nucleoside mixture was separated by
ultra-high performance liquid chromatography (UHPLC)
in less than 20 min and detected by a tandem mass
spectrometry (MS/MS) method that was recently pub-
lished (39). The geranyl modified nucleoside was con-
firmed using MS/MS where the molecular ions [MH+]
are fragmented at the glycosidic bond providing the prod-
uct ion [BH2+] and the neutral sugar residue. The re-
sultant [MH+]/[BH2+] ion-pair (Supplementary Table S1)
were then monitored using MRM. Individual MRMs
selected to verify the oligonucleotide composition and
successful incorporation of geranyl-nucleoside included
ges2U 397.3→265.1; G 284.1→152.1; A 268.2→136.0;
U 245.1→133.0; C 243.2→112.1 (Supplementary Figure
S26). S-2-thiouridine (ges2U) was detected only on the tar-
get oligo (Supplementary Figure S26A) in comparison to
the native RNA oligo, which was included as a negative con-
trol (Supplementary Figure S26B). The synthetic geranyl-
nucleoside, which is the 2-thio-geranylated product of com-
pound 4, was used to develop the MRM method and also
as our positive control (Supplementary Figure S26C).
CD analysis of geranylated RNA duplexes
We also checked the conformation of the geranylated RNA
duplexes in the context of both ges2U-A and ges2U-G pairs
by CD spectroscopy. As shown in Supplementary Figure
S28, both geranylated RNA duplexes showed very similar
conformation in comparison to their native counterparts. In
the U-A duplexes spectrum (Supplementary Figure S28A)
there is a strong positive peak around 270 nm, a relatively
weak negative peak around 240 nm and a weak positive
peak around 225 nm, all of which resemble the characteris-
tic peaks of the normal A-form structure in solution (40,41).
In comparison, the spectrum of U-G pair containing du-
plexes (Supplementary Figure S28B) shows that the gerany-
lated duplex retains a slightly better A-form conformation
than the native one based on a slight shift to 260 nm for
the strong positive peak, and the absence of the negative
peak at 240 nm and positive peak at 225 nm. The CD spec-
tra of nucleic acids are affected by many factors including
sequence, base stacking and conformation; given this, our
data indicates that the geranyl modification does not cause
gross perturbations in overall helical structures and folding
but does have some impact on local conformations.
Thermal denaturation and base pairing studies of geranyl–
RNA duplex
Molecular simulation of geranylated RNA duplexes and the
ribosomal binding of geranylated tRNA anticodon loop
With the geranylated RNA strand in hand, we studied
the base pairing stability and specificity of geranyl-uridine
(ges2U) against other bases through thermal denatura-
tion experiments. The UV-Tm curves of native and ger-
We further examined the structural features of geranyl-
modified RNA duplexes containing both ges2U-A and

Nucleic Acids Research, 2016 7
Table 1. Duplex stability and base pairing specificity of geranyl-2-thiouridine (ges2U) in the context of a 12mer RNA duplex 5ꢁ- GGACUXCUGCAG-3ꢁ
& 3ꢁ-CCUGAYGACGUC-5ꢁ (X pairs with Y)
Base pairs
c
Entry
X
Y
Tm (◦C)a
ꢁTm (◦C)b
−ꢁG◦
(kcal/mol)
37
1
2
3
4
U
U
U
U
A
G
C
U
60.8
57.9
48.3
50.4
18.6
16.9
11.9
13.4
−2.9
−12.5
−10.4
5
6
7
8
ges2U
ges2U
ges2U
ges2U
A
G
C
U
34.6
44.6
34.6
36.1
7.6
10.2
7.5
7.9
+10.0
0
+1.5
aThe Tm were measured in sodium phosphate (10 mM, pH 7.0) buffer containing 100 mM NaCl.
bꢁTm values are relative to the duplex with native U-A pair and ges2U-A pair respectively.
cObtained by non-linear curve fitting using Meltwin 3.5.
ges2U-G pairs using molecular simulations. Consistent
with our previous DNA work with geranyl modified
uridines, most of the ges2U–A pairs are in weakly paired
state with one or zero hydrogen bonds observed over the
course of our simulation, although two different hydrogen-
bonding modes were transiently observed with the N6 hy-
drogen of adenosine bonding to either N3 or O4 of ges2U
(Figure 2A and B). When the base-pairing is weak, the mod-
ified base with its hydrophobic tail fluctuates rapidly and
adopts a variety of random conformations, dramatically
distorting the local helical structure. This loss of hydrogen
bonding and distortion in the helical structure might be the
major reason that the ges2U-A pair containing duplex in
either A-form or B-form has a much lower Tm than their
native counterparts. In contrast, when the complementary
base is guanine, the geranyl-uracil ring is held in place by
two stable hydrogen bonds (Figure 2C) causing the orien-
tation of the hydrophobic tail to be more tractable and dic-
tated by the conformation of the duplexes. As shown in Sup-
plementary Figure S29, the geranyl modification breaks the
base-pairing of the uridine/thymidine with adenosine as ev-
idenced by the probability being highest for zero hydrogen
bonds. However, with the guanine nucleotide, the gerany-
lated group forms a stable base-pair in both the DNA and
RNA, as seen in the dominant probability for two hydrogen
bonds between the bases.
More interestingly, in the case of the B-form DNA, the
geranyl group was observed to be mainly accommodated in
the minor groove and could orient to both 5ꢁ and 3ꢁ direc-
tions (green and purple sticks in Figure 2D). In addition, the
geranyl group has strong interactions with the hydrophobic
pocket of the duplex, as indicated by the red colored region
in Figure 2D. The surface of the DNA and the RNA is col-
ored according to the amount of atomic contacts with the
geranyl group (red = high; blue = low). In the A-form RNA
duplex, where the hydrophobic pocket is dramatically di-
minished due to the presence of 2ꢁ-OH groups, the geranyl
group was observed to point out of the wide and shallow
minor groove of the helical structure and mainly point to
the 3ꢁ-end of the geranyl strand with backbone interactions
(Figure 2E). As a result, the overall duplex remains close to
the native one. Figure 2F shows rPP’, a plot of strand sep-
aration using the interstrand distances between the phos-
phate atoms along the duplex in both A-form and B-form
contexts. As expected, the strand separation is higher for the
A-form RNA as compared to the B-form DNA. The high-
lighted region shows the portion of the helices most affected
by the presence of the geranylated-thio modification. In the
case of the DNA, we observed a substantial difference in the
separation between the strands (the two blue curves), indi-
cating widening of the minor groove to accommodate the
hydrophobic geranyl group. In contrast, the minor groove
is not conducive for the binding of the hydrophobic tail in
the RNA, causing minimal changes in the interstand sep-
aration (the two red curves). These specific conformations
might also explain the Tm difference between the ges2U-G
and U-G in RNA duplex (∼13◦C) being higher than their
DNA counterparts (∼2◦C) (26). The favorable binding of
the geranyl group to the minor groove of the DNA keeps
the duplex almost as stable as the unmodified DNA, which
is consistent with the duplex stability enhancement of reg-
ular minor-groove binders (42), whereas the stability of the
modified RNA drops significantly compared to its unmod-
ified version.
To investigate the role of geranyl-2-thiouridine in
anticodon–codon recognition of tRNAs, we further per-
formed MD simulations of the ASL of tRNALys contain-
ing the modifications at the position 34. The 2-thiouridine
modification at the U34 position of tRNALysUUU is known
to be important for its codon recognition (43), and the
2-thio-group has also been shown to exist in its geranyl
form conjugating with other functionalities such as the
methyl-amino-methyl (mnm) group at the position 5 of the
uracil (17). Therefore, we studied the mnm-5-geranyl-2-thio
modified (mnm5ges2U34) and the unmodified versions of
tRNALysUUU in the presence of its cognate and near cognate
mRNA fragments at the A-site of ribosome using molecular
simulations. Two structures of 16S ribosomal subunit of T.
thermophilus containing the ASL of tRNALys
and the
UUU
mRNA codon fragment in the decoding center were used as
our starting models. The two structures differ in their codon
sequences (1XMO has AAG while 1XMQ has AAA as the
codon). As explained in the methods section, we used the
crystal structures and mutated U34 base to mnm5ges2U34
and performed all-atom MD simulations to compare the ef-
fect of ges2U modification on the U:A and U:G base pairs

8 Nucleic Acids Research, 2016
Figure 2. Molecular simulation studies of geranylated duplexes. (A and B) Proposed base pairing patterns between geranylated 2-thiouridine (ges2U)
and A with one hydrogen bond between either O4 or N3 of ges2U and N6 of A. (C) Proposed base pairing patterns between geranylated 2-thiouridine
(ges2U) and G with two stable hydrogen bonds. (D and E) Contact map of the geranyl group in the B-form DNA duplex and A-form RNA, respectively;
red = high, blue = low. In B-form DNA, the geranyl group fits well into the minor groove and interacts with the hydrophobic pocket (red/white colored
surface), pointing either to 5ꢁ or 3ꢁ-directions (green and purple sticks). In the RNA, the geranyl groups interact with the backbone oxygen atoms through
their methyl groups. The dominant orientation of the geranyl group in shown as green sticks. The yellow spheres represent the sulfur atom. (F) The duplex
separation plotted by the interstrand phosphate distances. For the B-form DNA, rPP’ is calculated as the distance between the ith phosphate group from
the 5ꢁ end of strand 1 and i-third phosphate group from the 3ꢁ end of strand 2. For the RNA, rPP’ is calculated as the distance between the ith phosphate
group from the 5ꢁ end of strand 1 and i-second phosphate group from the 3ꢁ end of strand 2. This choice corresponds to the phosphate group pairs that
are closest to each other.
that are directly involved in the codon–anticodon interac-
tions. Given the size of this system (∼2 million atoms in-
cluding solvent), a reversible binding simulation of the tR-
NAs to show differences in binding affinity is beyond the
scope of our work. Therefore, we performed nanosecond
timescale simulation of this system, which can specifically
answer the following two questions: (i) when modified with
the mnm5ges2U34 group, can U34 adopt conformations to
allow for stable Watson–Crick-like hydrogen bonds with the
G codon (44) at the ribosomal binding site? (ii) If so, can the
long hydrophobic geranyl group be accommodated at the
A-site without disruption of the codon–anticodon and ribo-
somal interactions? We used our simulation data to moni-
tor hydrogen bonding patterns between codon–anticodon
bases and ribosomal bases, and other structural changes
that occurred as a result of introducing the modified base
in the ASL. The distance and angle cut off for formation
of a H-bond were set at donor-acceptor (D-A) distance◦≤
As shown in Figure 3, our main result from these simula-
tions is that the hypermodified U34 shows weak hydrogen
bonding with A3 codon, whereas it maintains two Watson–
Crick-like hydrogen bonds with the G3 codon, similar to
the ones observed in the context of duplex. This behavior is
opposite to the unmodified U34 base, which prefers A3 over
G3. Specifically, for the first codon–anticodon pair (AAA-
UUU), A3-U34 base pair forms two H-bonds that were
dominantly observed through the course of the simulation.
However, introducing the mnm5ges2U modification in the
position 34 causes the A3-U34 base-pair to break, similar to
their behavior in the duplex simulations. In the second case
(AAG-UUU) with the wobble base pair G3-U34, primarily
two H-bonds are maintained during the simulation. As dis-
cussed before, the introduction of mnm5ges2U at position
34 changes the protonation state of atom N3 of U34. This
change in protonation state promotes Watson–Crick-like
hydrogen bonding pattern between the G-U base-pair, lead-
ing to a different set of D-H-A atoms (Supplementary Fig-
ure S30) and an increase in the probability of forming two
steady H-bonds through most of the duration of the simu-
lation. In addition, we find that the geranyl group can be ac-
commodated at the binding site, where it has stacking/van
der Waals interaction with the A4 codon and the residues
G530 and C1054 of the ribosome, while the 5-mnm group
interacts with the backbone phosphate group (Supplemen-
tary Figure S31). Furthermore, we also find that the riboso-
mal interactions, including A1492, A1493, G530 and C1054
with the mRNA and the tRNA are not disrupted during the
course of the simulation (Supplementary Figure S32).
Therefore, the MD simulations collectively suggest pos-
sible binding modes for the geranyl-modified tRNAs at the
wobble position, which might facilitate their selective codon
discrimination. While our simulations show that the long
hydrophobic geranyl group can possibly be accommodated
at the binding site, a systematic free-energy calculation is
needed to quantify the unfavorable free-energy associated
˚
3.3A and hydrogen-donor-acceptor (H-D-A) angle ≤ 30 .

Nucleic Acids Research, 2016 9
Figure 3. The (A–D) hydrogen bonding patterns for the the modified (mnm5ges2U34) and unmodified (U34) base with the A and G at the third position
of the codon. (E) Comparison of the numbers of hydrogen bonds percentages [#hb (0,1,2)] for each of the base pairs during the simulation time.
with introducing the modification. It has been proposed
that the geranyl-thio modification might be an intermediate
in conversion of 2-thiouridine to 2-selenouridine (23,24),
while it has also been shown to play a role in codon discrim-
ination (17). The hydrophobic terpene group might also be
specially evolved to fine-tune the efficiency and specificity
of codon–anticodon interactions during the translation or
play other important cellular functions. To further explore
these hypotheses and to truly understand the biological role
of this modification, we need to perform experimental bind-
ing studies of the tRNA to the ribosome and/or more ex-
tensive simulations (e.g. in the presence of a longer mRNA
fragment with the 70S ribosome), as well as the complex
structure studies, which are currently being pursued in our
lab.
detailed investigation of this unique natural modification in
RNA will provide new insights into its current biological
functions, and the potential evolutionary roles in lipid syn-
thesis in the original stages of the RNA world.
SUPPLEMENTARY DATA
Supplementary Data are available at NAR Online.
ACKNOWLEDGEMENTS
We thank Leah Seebald and Prof. Daniele Fabris for the
help in mass spec analysis. This work used computing re-
sources from the Extreme Science and Engineering Discov-
ery Environment (XSEDE).
FUNDING
CONCLUSION
University at Albany, State University of New York start-up
fund (to J.S.); PhRMA Foundation (to A.C.); Simons Foun-
dation Postdoctoral Fellowship [338863 to R.W.]. Funding
for open access charge: University at Albany start-up fund.
Conflict of interest statement. None declared.
In this work we have synthesized geranylated RNA, studied
their base pairing stability and specificity, and investigated
their structural features in both duplexes and ribosome con-
texts. Our biophysical and molecular simulation studies col-
lectively showed that this hydrophobic terpene group, a re-
cently discovered natural RNA post-transcriptional mod-
ification, results in a much higher thermostability of U-G
pair over the normal Watson–Crick U-A pair and other
mispairs, indicating a strong base pairing specificity and
discrimination between G and other nucleobases in both
duplex structures and the codon–anticodon recognition
in the presence of ribosome binding. The two hydrogen
bonds formed between the geranylated 2-thiouridine and
the guanosine base are dominantly stable in all the struc-
tural contexts we studied. This work provides the explana-
tion to why there is better recognition of G-ending codes
over the others by geranylated tRNAs. Besides enhancing
the base pairing specificity, this bulky hydrophobic geranyl
group has been speculated to play other functions, such
as RNA localization and RNA transportation, as well as
geranyl- and seleno-involved metabolic pathways. Further
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