Unwinding DNA and RNA with Synthetic Complexes: On the Way to Artificial Helicases

Article abstract of DOI:10.1002/chem.201502738

Synthetic helicases can be designed on the basis of ligands that bind more strongly to single-stranded nucleic acids than to double-stranded nucleic acids. This can be achieved with ligands containing phenyl groups, which intercalate into single strands, but due to their small size not into double strands. Moreover, two phenyl rings are combined with a distance that allows bis-intercalation with only single strands and not double strands. In this respect, such ligands also mimic single-strand binding (SSB) proteins. Exploration with more than 23 ligands, mostly newly synthesised, shows that the distance between the phenyl rings and between those and the linker influence the DNA unwinding efficiency, which can reach a melting point decrease of almost ΔT_m=50°C at much lower concentrations than that with any other known artificial helicases. Conformational pre-organisation of the ligand plays a decisive role in optimal efficiency. Substituents at the phenyl rings have a large effect, and increase, for example, in the order of Hm=48°C), whereas the AT strand remains untouched, and with poly(rA)-poly(rU) as an RNA model one observes unfolding at 29°C with a concentration of only 30 μM. Sit back, relax! Unwinding of nucleic acid double helices into single strands by helicases plays an important role in many processes. Synthetic helicases can be designed with ligands containing phenyl groups that intercalate only into single strands (see figure). The best ligand lowered the melting points of double strands by 48°C at a ligand concentration of only 40 μM, and could discriminate between AT and GC homopolymers.

Full text of DOI:10.1002/chem.201502738

DOI: 10.1002/chem.201502738
Full Paper
&
Helical Structures
Unwinding DNA and RNA with Synthetic Complexes: On the Way
to Artificial Helicases
[
a]
Martin Gasiorek and Hans-Jçrg Schneider*
Abstract: Synthetic helicases can be designed on the basis
of ligands that bind more strongly to single-stranded nucleic
acids than to double-stranded nucleic acids. This can be ach-
ieved with ligands containing phenyl groups, which interca-
late into single strands, but due to their small size not into
double strands. Moreover, two phenyl rings are combined
with a distance that allows bis-intercalation with only single
strands and not double strands. In this respect, such ligands
also mimic single-strand binding (SSB) proteins. Exploration
with more than 23 ligands, mostly newly synthesised, shows
that the distance between the phenyl rings and between
those and the linker influence the DNA unwinding efficiency,
508C at much lower concentrations than that with any other
known artificial helicases. Conformational pre-organisation
of the ligand plays a decisive role in optimal efficiency. Sub-
stituents at the phenyl rings have a large effect, and in-
crease, for example, in the order of H<F<Cl<Br, which il-
lustrates the strong role of dispersive interactions in interca-
lation. Studies with homopolymers revealed significant selec-
tivity: for example, with a ligand concentration of 40 mm at
358C, only GC double strands melt (DT =488C), whereas
m
the AT strand remains untouched, and with poly(rA)–poly(rU)
as an RNA model one observes unfolding at 298C with a con-
centration of only 30 mm.
which can reach a melting point decrease of almost DT =
m
Introduction
1
5 mm are required and these compounds show relatively
[
8]
small melting point changes. The effect of small alkylammo-
nium ions on double strands has been investigated, but the
DTm decrease was very small, for example, 28C at 0.1m; an in-
creased efficiency with GC-rich strands was, however, also ob-
The unwinding of nucleic acid double helices into single
strands by helicases plays an important role in many genetic
processes, for example, in DNA replication, recombination,
repair, and transcription. This is illustrated by more than 10000
publications to date with helicases in the title, almost entirely
[
10]
served.
Later, much more dramatic and selective DTm
changes were achieved with highly charged alkylammonium
[
1]
devoted to the action of the corresponding enzymes. Dis-
derivatives, for example, DT =418C for RNA and DT =18C
m
m
[
2]
[11]
ease-related helicases are also the focus of several reviews.
RNA helicases that maintain proper folding have recently re-
for DNA;
some macrocyclic alkylammonium derivatives
showed an inverse preference for base flipping with DT =
m
[3]
ceived particular attention. The unwinding of the folded nu-
cleic acids is controlled by enzymes that couple the chemical
energy derived from nucleoside triphosphate hydrolysis to the
À68C for RNA and DT =268C for DNA analogues (values at
m
[
12]
a ligand to nucleic acid ratio, r, of 0.3). These distinct melting
point changes could be rationalised by considering ligand fit-
[1,4]
[11,12]
otherwise non-spontaneous unwinding reaction.
Typically
ting to the different DNA- and RNA-like grooves.
aromatic-rich loops, which can intercalate into DNA strands,
Somewhat closer to natural systems are simple aromatic
amino acid amides, which, although at the relatively high con-
centration of 1 mm, lower melting points of poly(A)–poly(U)
[5]
are found in DNA helicases; helicases generally bind with
higher affinity to single-stranded (ss) DNA than to double-
[
1]
[13]
stranded (ds) DNA. To the best of our knowledge, to date,
there have been no systematic attempts to design efficient ar-
tificial helicases. A few compounds have been reported for un-
and poly(I)–poly(C) double strands. New artificial helicases
can be designed on principles related to natural systems: sta-
bilisation of ss-nucleic acids by interactions with stacking aro-
matic components. Our approach to more efficient artificial
helicases is based on the use of double intercalators, which
have two arenes at a distance that allows double intercalation
into the more flexible single strands, but not into double
[
6]
winding ds-nucleic acids. These comprise metal complexes;
[7]
small single arenes, such as ethidium bromide (EB); cyclodex-
[
8]
[9]
trin; and peptide nucleic acids. Concentrations of up to
[
14]
[
a] Dr. M. Gasiorek, Prof. Dr. H.-J. Schneider
strands due to the next-neighbour exclusion principle.
FR Organische Chemie, Universität des Saarlandes
Therefore, our ligands also mimic single-strand binding (SSB)
proteins. In addition, we use as arenes phenyl units that do
not intercalate, even as single units, into double strands, due
to a too small gain in stacking energy, which cannot compen-
sate for the destacking of nucleobases and the loss of Watson–
6
6041 Saarbrücken (Germany)
E-mail: ch12hs@rz.uni-sb.de
Supporting information for this article is available on the WWW under
http://dx.doi.org/10.1002/chem.201502738. It contains full experimental de-
tails.
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Crick hydrogen bonds in the
[
15,16]
double strand.
Systematic
investigations showed previously
that only indole-sized or larger
arenes were capable of inserting
into ds-nucleic acids, and only at
[16]
higher concentrations.
Sub-
stituents on the phenyl groups
can further enhance the stacking
energy and provide highly effi-
cient synthetic helicases; these
may be used for many applica-
tions, such as the polymer chain
reaction (PCR) or the production
of oligo- and polynucleotides,
which require the unwinding of
ds-nucleic acids. Another interest
was the possibility of unwinding
selectively either the GC- or AT-
rich parts in DNA.
Results and Discussion
Model investigations
Preliminary computer simula-
tions suggested that ligands
containing two phenyl rings at
a distance of about 2 Š and pos-
itively charged nitrogen atoms
distant from the arenes would,
according to our concept, be
best suited to serve as artificial
helicases. Accordingly, a large
number of mostly new com-
pounds (see Scheme 1 and
Scheme S1 in the Supporting In-
formation) were prepared by
standard procedures, usually by
condensation of the correspond-
ing aldehydes and amines, or by
the reaction of esters and
amines with subsequent reduc-
tion (see the Supporting Infor-
mation). NMR spectroscopy titra-
tions with, for example, 5’-ade-
nosine monophosphate (5’AMP)
as a model for stacking between
Scheme 1. Ligands used for destabilisation of ds-nucleic acids. Italic numbers indicate the approximate concentra-
tion (in mm) needed for a melting decrease of DT
values are given if DT
=À228C could not be reached. Missing numbers, indicated by (a), were not measurable;
two phenyl rings, with ligand 1a see Table S4 in the Supporting Information.
m
=228C with ds-CT-DNA (CT=calf thymus); alternatively other
m
showed
a
complexation free
À1
energy of DG=À7.3 kJmol .
With compounds 1c, 1d, 1g and 2b, which all have substitu-
troscopy titration of 1c with electroneutral adenosine gave
À1
À1
À1
ents at the phenyl groups, higher values of 8.2 to 9.9 kJmol
DG=3.5 kJmol ; a difference of about 5 kJmol in compari-
son to 5’AMP is in agreement with a single ion-pair contribu-
tion.
1
were obtained. H NMR chemical shifts calculated for 100%
[
17]
complexation showed shielding values of up to À0.47 ppm at
the ligands, as a result of the shielding cone of the adenine
ring (Table S1 in the Supporting Information). An NMR spec-
As another model, the trinucleotide dApdApdA was
complexed with ligand 1g; a higher affinity is expected
through increased ion pairing. The difference between the ob-
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À1
served DG value of 10 kJmol and the value with AMP (for 1g
8
To compare the helicase efficiency of the different com-
pounds Scheme 1, the values in italics show the approximate
concentrations (in mm) needed for a melting decrease of
À1
.1 kJmol ) indicates only moderately enhanced ion pairing
due to the presence of more charges in the trinucleotide.
DT =À228C (see also Table S3 in the Supporting Information),
m
or alternatively the DTm at a given concentration (Table S4 in
the Supporting Information). The most effective ligands were
those containing two aryl rings connected in the meta 1,3-po-
sition by a dialkylamino spacer to a phenyl ring (ligands 1a–
1g, 2, 3, and 6–8). All other structures required ligand concen-
Melting decrease of ds-nucleic acids
The helicase activity of the compounds listed in Scheme 1 and
Scheme S1 in the Supporting Information was tested as usual
by monitoring changes of the UV extinction as a function of
temperature (Figure 1). The affinity of selected ligands to ds-
trations above 0.5 mm for a change of DT
=À228C, although
m
ligand flexibility would partially allow stacking with a nucleo-
base (see also Scheme S1 in the Supporting Information). That
conformational pre-organisation plays a decisive role is visible,
for example, in the relatively small DTm values for open-chain
ligands, such as 9c or 4. Compounds such as 5a or 5b, with
substitution in the para 1,4-position, are also much less active.
The length of the spacer has a distinct effect, as seen in the
difference between 1a (2.0 mm), 2a (0.3 mm), and 3 (0.1 mm):
the short spacer (1a) allows bis-intercalation into the single
strand only with conformational distortion.
Figure 1. Melting curves of CT-DNA with ligand 1c showing relative extinc-
À5
tion values versus temperature [8C]: [CT-DNA]=7.6”10 m; concentrations
of 1c [mm] of a) 0.0, b) 0.02, c) 0.04, and d) 0.06; 2-(N-morpholino)ethanesul-
fonic acid (MES) buffer; pH 6.25; for the experimental method, see refs. [11d]
and [11e].
DNA was assessed by displacement assays of the fluorescence
Figure 2. Intercalation of ligand 1c into ss-DNA (tentative simulation with
the CHARMM force field, without energy minimisation).
À4
dye EB; these showed C50 values of around 1 to 5”10 m for
the investigated ligands (Table S2 in the Supporting Informa-
tion), which were close to those measured for many other li-
[
12c]
gands with two ammonium centres.
Oligo- and polyamines
Figure 2 illustrates the corresponding insertion mode. The
intercalation mode was supported by preliminary NMR spec-
troscopy studies, which, with related compounds, showed up-
field shifts for the ligand protons induced by the ring current
of the nucleobases, similar to model complexes with 5’AMP
usually lead to enhanced melting points of ds-nucleic acids,
[
12c]
which parallels their affinities to, for example, CT-DNA.
In
contrast, the compounds in Scheme 1 showed a melting point
decrease, DT , of between 0 and 488C, depending on the
m
[
15]
ligand structure and concentration (Table S3 in the Supporting
Information), and there was no correlation between C50 affinity
values and DTm (Table S2 in the Supporting Information). At
lower concentration of the ligands, one observes a small stabi-
lisation of ds-CT-DNA, which is typical for all kinds of ammoni-
um derivatives. Only if the ligand concentration comes closer
to saturation (with r values of around 0.4; see Table S4 in the
Supporting Information) does unfolding start, and reaches
a maximum at r values of around five, depending to some
degree on the ligand structure. In some cases, as with ligand
(see above, Table S1 in the Supporting Information). As with
all associations between nucleic acids and amino ligands, the
activity of the ligands depends on the ionic strength due to
competing cation binding (Figure 3). The observed sensitivity
reflects that observed with other amines for the ion-pairing
[
18]
strength as a function of ionic strength.
Substituent effects: dispersive interactions
A striking efficiency increase was observed when the intercalat-
8
c, at higher concentration the melting curves did not show
ing phenyl rings were equipped with halogen substituents (1c,
the usual sigmoidal shape (Figure S1 in the Supporting Infor-
1d, 2b, 6), for example, 30 mm of 1d already led to DT =
m
mation), which makes the determination of an exact DT value
228C. A better comparison between the effects of heterosub-
stitution is possible if one compares the ligand effects at
50 mm for 1c (R=Cl: DT =À238C) and 1d (R=Br: DT =
m
difficult. The efficiency of the ligands in terms of concentration
needed for unwinding and in terms of the rates is clearly
a function of the difference in binding energies between
single and double strands.
m
m
À358C): the fluorine derivative, 1b, requires a tenfold higher
concentration (0.5 mm) for DT =À268C, whereas for R=OMe
m
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Figure 3. Dependence of DT
m
on ionic strength, I. Measured for ligand 1c
À5
À5
(
0.06 mm) with NaCl, [CT-DNA]=7.6”10 ; MES buffer; pH 6.25.
Figure 4. Melting rates of ds-CT-DNA (7.7”10 m) with ligand 1c in MES
buffer at pH 6.25; extinction, E, was measured at l=260 nm for concentra-
tions of 1c [mm] of a) 60, b) 70, c) 80, and d) 120 at 208C, and e) 120 at
158C.
(
1g) one observes DT =À358C at 0.5 mm. The activ-
m
ity sequence Br>Cl@F@H and the OMe effect (1g)
[
a]
agrees well with recently derived numbers for disper-
Table 1. Unfolding of homopolymers as DNA and RNA models.
[19]
sive interactions of corresponding derivatives, and
illustrates the importance of such van der Waals
forces in nucleic acid intercalation. Derivatives con-
[b]
[c]
[d]
Ligand
r
CT-DNA
p(dA)·p(dT)
p(dG)·p(dC)
p(rA)·p(rU)
0
0
0
0.52
0.65
1
1
2
0.13
0.26
.13
.26
.39
+4
À2
À6
À9/+5
À22/+5
À30/+5
À37
taining substituents such as NO or iodine (1e, 1h)
[e]
2
À36
À10
[
e]
e]
should, in view of their polarisability, also be effec-
tive, but could not be used due to solubility prob-
lems.
À43
À48
2
b
[
[
e]
.0
.5
.0
À13
À21
À22
<À48
The kinetics of unfolding were studied with CT-
DNA and ligand 1c. Figure 4 illustrates the time de-
pendence of denaturation on ligand concentration.
The curves indicate that at 0.12 mm, the concentra-
tion at which formally all nucleotides can be occu-
pied by ligand (r=[ligand]/[DNA-phosphate]=1.5),
the half-lifetime is about 1 min, which increases to
about 30 min at 0.08 mm. However, even after 1 h,
the ds-DNA is not completely molten in 0.12 mm 1c.
The change of free ligand concentration during the
reaction and the UV extinction change with ss-DNA
alone (Figure S3 in the Supporting Information) pro-
hibits fitting to first-order kinetics. Instead, initial
rates were taken from the curves with ligand 1c
within a time period in which the free ligand concen-
+1
+1
À2
À4
À6
[
e]
[f]
0.39
0.52
0.65
À21 /+1
[e]
[e]
À29 /+1
À33
1d
[e]
[e]
À35
À40
[e]
[e]
1.0
1.5
2
À19
À23
À27
À46
.0
À5
[a] Measured with a ds-nucleic acid concentration of 7.6”10 m in MES buffer at
pH 6.25; error in DT =0.58C. [b] Poly(dA)–poly(dT). [c] Poly(dG)–poly(dC). [d] Poly(rA)–
poly(rU). [e] Error in DT =18C. +: if unfolding occurs at r=[Ligand]/[DNA-phos-
phate]<1 (see, for example, Figure 1c), one observes two phases: first stabilisation
positive DT , for example, between 1 and 58C) and then destabilisation (negative
DT
=À4 to À488C). [f] Atypical curve.
m
m
(
m
m
tration remained relatively constant; the corresponding rate
constants, k (Table S5 and Figure S2 in the Supporting Informa-
tion), increased by a factor of two orders of magnitude from
of folded regions in DNA, which are either rich in A and T, or in
G and C bases, or are based on A and U in RNA.
With respect to DNA models, one recognises that the effi-
ciency of both 1b and 2b (Table 1) is much smaller for
6
0 mm of 1c to 120 mm.
poly(dA)–poly(dT) (T =458C) than that for poly(dG)–poly(dC)
m
(
Tm =788C). The efficiency for CT-DNA is between that of the
two homopolymers and reflects the varying content of
poly(dA)–poly(dT) and poly(dG)–poly(dC) in the natural double
helix. The stronger helicase activity towards the poly(dG)–
poly(dC) duplex is remarkable, particularly in view of the
higher stability of GC duplexes, which until recently was be-
lieved to be due to the presence of three instead two hydro-
gen bonds in AT pairs. Recently, it was shown that stacking,
which is one of the most important effects in nucleic acid in-
Selectivity: Measurements with ds-homopolymers as DNA
and RNA models
Measurements with synthetic homopolymers allowed the
study of the selectivity of the artificial helicases; this might
also be of interest for some applications, for example, for the
selective opening of DNA duplexes or for the manipulation of
[20]
DNA-based nanostructures. Because no hydrogen bonding is
involved in the action of the ligands, a significant sequence se-
lectivity is not expected, but can result from different stabilities
[
21]
teractions,
and not base pairing was the major factor in
duplex stabilisation, and that this was stronger with GC than
Chem. Eur. J. 2015, 21, 18328 – 18332
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[
22]
that with AT. This would also mean that stacking in ss-GC is
stronger than that in ss-AT sequences, which is in agreement
with the finding that the efficiency of our stacking-based artifi-
cial helicases is higher with GC homopolymers. Measurements
with the RNA model, poly(rA)–poly(rU), are hampered by its
low melting point (358C), but at comparable concentrations
[5] K. A. Manthei, M. C. Hill, J. E. Burke, S. E. Butcher, J. L. Keck, Proc. Natl.
Acad. Sci. USA 2015, 112, 4292–4297; A. C. W. Pikea, G. Shivasankari, P.
Swuecc, M. Bertib, Y. Zhanga, C. Schneckea, F. Marinod, F. von Delfta, L.
Renaultc, A. Costac, O. Gileadia, A. Vindigni, Proc. Natl. Acad. Sci. USA
2015, 112, 4286–4291.
[6] E. Kimura, T. Iked, M. Shionoya, Pure Appl. Chem. 1997, 69, 2187–2195;
B. Sarkar, P. Mukhopadhyay, P. K. Bharadwaj, Coord. Chem. Rev. 2003,
2
2
36, 1–13; T. Chandrasekar, N. Pravin, N. Raman, Inorg. Chem. Commun.
014, 43, 45–50; T. Suchµnkovµ, K. Kubicek, J. Kasparkova, V. Brabec, J.
(
or r values) both 1d and 2b exhibit less helicase activity than
that with the DNA models.
Inorg. Biochem. 2012, 108, 69–79.
[
[
7] M. Hayashi, Y. Harada, Nucleic Acids Res. 2007, 35, e125.
8] S. S. Jaffer, P. Ghosh, A. Das, P. Purkayastha, Nanoscale 2010, 2, 1420–
Conclusion
1422.
[
9] M. Komiyama, Y. Aiba, Y. Yamamoto, J. Sumaoka, Nat. Protoc. 2008, 3,
The use of small arenes that only intercalated into ss-nucleic
acids, in combination with bis-intercalators, which could not
intercalate into double strands due to the neighbour exclusion
principle, led to artificial helicases of hitherto unsurpassed ac-
tivity. Substituents such as halogens in the aryl rings increased
the activity due to large dispersive interactions. The new li-
gands lend themselves to a variety of possible applications,
such as the preparation of single strands from DNA in the PCR.
Because the ligands have two positive charges, they can be
easily removed from the unfolded nucleic acids. A combination
of several bis-intercalators could further increase the activity.
The remarkable nucleobase selectivity allows AT-rich strands to
be separated from GC-rich strands. In view of this, the GC-rich
655–662.
[10] W. B. Melchior Jr, P. H. von Hippel, Proc. Natl. Acad. Sci. USA 1973, 70,
98–302; see also A. D. Voskoboinik, D. R. Monaselidze, G. N. Mege-
2
ladze, Z. I. Chanchalashvili, Y. S. Lazurkin, M. D. Frankamenetskii, Mol.
Biol. 1975, 9, 628–633.
[11] a) N. Lomadze, H.-J. Schneider, M. T. Albelda, E. García-EspaÇa, B. Verde-
jo, Org. Biomol. Chem. 2006, 4, 1755–1759; b) see also A. Slama-
Schwok, F. Peronnet, E. Hantz-Brachet, E. Taillandier, M. P. Teulade-
Fichou, J. P. Vigneron, M. BestBelpomme, J.-M. Lehn, Nucleic Acids Res.
1997, 25, 2574–2581; c) D. K. Chand, H.-J. Schneider, A. Bencini, A. Bian-
chi, C. Giorgi, S. Ciattini, B. Valtancoli, Chem. Eur. J. 2000, 6, 4001–4008;
d) D. K. Chand, H.-J. Schneider, J. A. Aguilar, F. Escartí, E. García-EspaÇa,
Inorg. Chim. Acta 2001, 316, 71–78.
[
12] a) M. Fernandez-Saiz, H.-J. Schneider, J. Sartorius, W. D. Wilson, J. Am.
Chem. Soc. 1996, 118, 4739–4745; b) K. Li, M. Fernandez-Saiz, C. T. Rigl,
A. Kumar, K. G. Ragunathan, A. W. C. McConnaughie, D. W. Boykin, H.-J.
Schneider, W. D. Wilson, Bioorg. Med. Chem. 1997, 5, 1157–1172; c) E.
Garcıa-Espana, I. Piantanida, H.-J. Schneider in Supramolecular Systems
in Biomedical Fields; Nucleic Acids as Supramolecular Targets (Ed.: H.-J.
Schneider), Royal Society of Chemistry, Cambridge, 2013, pp. 213–258.
[23]
quadruplexes in telomeres
could also be an interesting
target of ligands such as 1c. Attachment of nucleic acid or
peptide nucleic acid (PNA) oligomers may allow sequence se-
lectivity by Watson–Crick hydrogen bonding in the future.
[13] D. Pçrschke, M. Jung, Nucleic Acids Res. 1982, 10, 6163–6176.
14] A. Ali, M. Gasiorek, H.-J. Schneider, Angew. Chem. Int. Ed. 1998, 37,
016–3019; Angew. Chem. 1998, 110, 3183–3186.
[15] J. Sartorius, H.-J. Schneider, FEBS Lett. 1995, 374, 387–392.
[
3
Acknowledgements
[
16] H.-J. Schneider, J. Sartorius, J. Chem. Soc. Perkin Trans. 2 1997, 2319–
327.
2
This work has been supported by grants from the Deutsche
Forschungsgemeinschaft and the VW foundation.
[
17] H.-J. Schneider, Angew. Chem. Int. Ed. 2009, 48, 3924–3977; Angew.
Chem. 2009, 121, 3982–4036.
[
[
[
18] A. Md. Hossain, H.-J. Schneider, Chem. Eur. J. 1999, 5, 1284–1290.
19] H.-J. Schneider, Acc. Chem. Res. 2015, 48, 1815–1822.
20] N. C. Seeman, Annu. Rev. Biochem. 2010, 79, 65; T. Schnitzler, A. Herr-
mann, Acc. Chem. Res. 2012, 45, 1419; F. C. Simmel, Curr. Opin. Biotech-
nol. 2012, 23, 516; V. Linko, H. Dietz, Curr. Opin. Biotechnol. 2013, 24,
555–561; L. Zhou, A. E. Marras, H.-J. Su, C. E. Castro, Nano Lett. 2015,
15, 1815–1821; T. Gerling, K. F. Wagenbauer, A. M. Neuner, H. Dietz, Sci-
ence 2015, 347, 1446–1452.
Keywords: artifical enzymes · dispersive interactions · DNA ·
helicases · intercalation · polymers · RNA
[
1] For reviews, see: DNA Helicases and DNA Motor Proteins, Advances in Ex-
perimental Medicine and Biology, Vol. 973 (Ed.: M. Spies), Springer,
Berlin, 2013; C. G. Wu, M. Spies, Adv. Exp. Med. Biol. 2013, 973, 1–16; M.
Abdelhaleem, Methods Mol. Biol. 2009, 587, 1–12; D. L. Croteau, V.
Popuri, P. L. Opresko, V. A. Bohr, Annu. Rev. Biochem. 2014, 83, 519–552;
M. R. Singleton, M. S. Dillingham, D. B. Wigley, Annu. Rev. Biochem. 2007,
[21] G. M. Blackburn, M. J. Gait, D. Loakes, D. M. Williams Nucleic Acids in
Chemistry and Biology, 3rd ed., RSC, Cambridge, 2006; K. Riley, P. Hobza,
Acc. Chem. Res. 2013, 46, 927–936; J. Sponer, J. E. Sponer, A. Mladek, D.
Arnost, Biopolymers 2013, 99, 978–988; D. Duzdevich, S. Redding, E. C.
Greene, Chem. Rev. 2014, 114, 3072–3086.
[22] P. Yakovchuk, E. Protozanova, M. D. Frank-Kamenetskii, Nucleic Acids Res.
2006, 34, 564–574.
[23] K. Paeschke, K. R. McDonald, V. A. Zakian, FEBS Lett. 2010, 584, 3760–
3772, and references therein.
7
6, 23–50; A. Mentes, A. M. Florescu, E. Brunk, J. Wereszynski, M.
Joyeux, I. Andricioaei, Biopophys. J. 2015, 108, 1727–1738; D. Lenglet,
M.-H. David-Cordonnier, J. Nucleic Acids 2010, 2010, 1–17.
[
2] E. Jankowsky, M. E. Fairman, Curr. Opin. Struct. Biol. 2007, 17, 316–324;
J.-B. Vannier, G. Sarek, S. J. Boulton, Trends Cell. Biol. 2014, 24, 416–425;
M. H. Upadya, J. J. Aweya, Y.-J. Tan, World J. Gastroenterol. 2014, 20,
2
913–2926; N. E. Simon, A. Schwacha, BioMed. Res. Int. 2014, 549719.
[
[
3] I. Jarmoskaite, R. Russell, Annu. Rev. Biochem. 2014, 83, 697–725; A. L.
Leit¼o, M. C. F. J. Enguita, Int. J. Mol. Sci. 2015, 16, 2269–2293; J.
Robert-Paganin, S. Rety, N. Leulliot, BioMed Res. Int. 2015, 931857.
4] B. Bhattacharyya, J. L. Keck, Protein Sci. 2014, 23, 1498–1507.
Received: July 12, 2015
Published online on October 27, 2015
Chem. Eur. J. 2015, 21, 18328 – 18332
www.chemeurj.org
18332
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