Stereochemistry of benzylic carbon substitution coupled with ring modification of 2-nitrobenzyl groups as key determinants for fast-cleaving reversible terminators

Article abstract of DOI:10.1002/anie.201106516

A complete set of 2-nitrobenzyl-modified reversible terminators have been developed, which upon exposure to UV light generate natural hydroxymethyl nucleotides (see scheme). The combination of a stereospecific (S)-tert-butyl group (R) at the benzylic carb

Full text of DOI:10.1002/anie.201106516

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DOI: 10.1002/anie.201106516
Lightning Terminators
Stereochemistry of Benzylic Carbon Substitution Coupled with Ring
Modification of 2-Nitrobenzyl Groups as Key Determinants for Fast-
Cleaving Reversible Terminators**
Brian P. Stupi, Hong Li, Jinchun Wang, Weidong Wu, Sidney E. Morris, Vladislav A. Litosh,
Jesse Muniz, Megan N. Hersh, and Michael L. Metzker*
Next-generation sequencing (NGS) technologies have facili-
tated important biomedical discoveries, yet high error rates
and slow cycle times warrant further improvements in the
chemistry.[1a] Such technologies that employ the cyclic rever-
sible termination (CRT) method[1a,b] typically utilize 3’-O-
blocked reversible terminators.[2a–c] Recently, we described a
novel 3’-OH-unblocked reversible terminator based on 2-
of developing a complete set of reversible terminators
(Figure 1).
Ideally, these terminators should exhibit fast nucleotide-
incorporation kinetics, single-base termination, high nucleo-
tide selectivity, and rapid terminating group cleavage. For the
latter, the degree to which the rate of photochemical cleavage
is altered depends on numerous factors including substitution
of the benzylic carbon,[10a–c] attachment of functional group(s)
to the benzyl ring,[10b–d] and nature of the leaving group,[10a] as
well as pH,[10a,d,e] solvent,[10c,f,g] and light intensity.[10e,g] One
nitrobenzyl-modified
5-hydroxymethyl-2’-deoxyuridine
(HOMedU) 5’-triphosphate.[3] Our study revealed that the
proximity of the 2-nitrobenzyl group to the nucleobase and
the size of the alkyl group attached to its a-methylene carbon
are important structural features that confer the unique
properties of single-base termination, efficient incorporation,
and high nucleotide selectivity (i.e., high fidelity) to these 3’-
OH-unblocked nucleotides.[3] These properties have the
potential to improve accuracy and read-lengths in the CRT
method. As HOMedU is a naturally found hypermodified
nucleoside,[4a] we set out to identify other such examples. 5-
Hydroxymethyl-2’-deoxycytidine (HOMedC) is found natu-
rally in the genomes of T-even bacteriophages[4a,b] and
mammals.[5] Pyrrolopyrimidine (7-deazapurine) is also found
naturally in nucleoside antibiotics[6] and tRNAs.[7] Thus,
various analogues of 2-nitrobenzyl-modified 7-deaza-7-
hydroxymethyl-2’-deoxyadenosine
(C7-HOMedA),[8]
HOMedC, 7-deaza-7-hydroxymethyl-2’-deoxyguanosine (C7-
HOMedG),[9] and HOMedU were synthesized with the goal
[*] B. P. Stupi, Dr. H. Li, J. Wang, Dr. W. Wu, S. E. Morris,
Prof. V. A. Litosh,[+] Dr. M. N. Hersh, Prof. M. L. Metzker
LaserGen, Inc.
Houston, TX 77054 (USA)
S. E. Morris, J. Muniz, Prof. M. L. Metzker
Human Genome Sequencing Center (USA)
Prof. M. L. Metzker
Department of Molecular & Human Genetics
Baylor College of Medicine
One Baylor Plaza, N1409, Houston, TX 77030 (USA)
E-mail: mmetzker@bcm.edu
[+] Department of Medicinal Chemistry and Pharmacognosy
University of Illinois, Chicago, IL 60612 (USA)
Figure 1. Structures of 2-nitrobenzyl-modified HOMedNTP analogues,
called Lightning Terminators (LT). R=H, isopropyl, or tert-butyl;
R’=H, 4-OMe, 5-OMe, 4,5-di-OMe, or 6-NO2; see keys for specific
examples. “*” denotes two different diastereomers (R and S). Red
chemical structures denote terminating functional groups that are
cleaved upon exposure to UV light. Syntheses of all nucleotides are
described in the Supporting Information, except for those of dU.I and
dU.V, which have been previously reported.[3]
[**] This work was supported in part by the National Institutes of Health
(R01 HG003573). We thank Sherry Metzker from LaserGen for
critical reading of the manuscript.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201106516.
Re-use of this article is permitted in accordance with the Terms and
Conditions set out at http://angewandte.org/open.
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property, however, that has not been studied is stereochem-
istry, whereby substitution of 2-nitrobenzylꢀs benzylic or a-
carbon results in a chiral center. For the case of nucleotide
synthesis, coupling of a racemic a-substituted 2-nitrobenzyl
alcohol would result in two diastereomers, which differ only
by the absolute configuration (R or S) at the benzylic carbon
(“*” in Figure 1). Here, we describe our efforts toward
improving the photochemical-cleavage properties by exam-
ining various ring-substituted, stereospecific a-isopropyl- and
a-tert-butyl-2-nitrobenzyl-modified reversible terminators.
Unlike our work with a-substituted HOMedU ana-
logues,[3] we identified chromatographic conditions to sepa-
rate C7-HOMedA analogues into single diastereomeric
nucleotides, with the first eluting isomer denoted as ds1 and
the second as ds2. To evaluate photochemical-cleavage
effects, three 2-nitrobenzyl-modified C7-HOMedA analogues
were synthesized and separated into single diastereomers,
dA.III.a (a-isopropyl), dA.III.b (a-isopropyl-4-OMe), and
dA.III.c (a-isopropyl-6-NO2), along with the parent dA.I (see
the Supporting Information). These C7-HOMedATP ana-
logues were applied in incorporation assays followed by
photochemical-cleavage experiments in sodium azide solu-
tion (Table 1). In all cases, the ds2 isomers of dA.III.a,
dA.III.b, and dA.III.c showed faster photochemical cleavage
4.5, 4.4, and 3.0, respectively, compared with their ds1
counterparts (Table 2). The photochemical-cleavage rates of
both 5-OMe ds1 and ds2 isomers were 1.4 times faster than
those of their respective 4-OMe isomers, demonstrating that
Table 2: Rates of photochemical cleavage for C7-HOMedG analogues.
C7-HOMedG Analogue
DT50 in 1 mm NaN3
No DTT
50 mm DTT
dG.I
9.2Æ0.3
11.0Æ0.4
3.6Æ0.3
4.9Æ0.3
1.1Æ0.1
3.5Æ0.3
0.8Æ0.1
2.4Æ0.1
0.8Æ0.1
8.1Æ0.2
10.7Æ0.2
3.5Æ0.3
4.6Æ0.3
1.3Æ0.2
3.0Æ0.1
0.8Æ0.1
2.3Æ0.2
0.8Æ0.1
dG.V.a ds1
dG.V.a ds2
dG.V.b ds1
dG.V.b ds2
dG.V.c ds1
dG.V.c ds2
dG.V.d ds1
dG.V.d ds2
ring position influences the cleavage rate. The bis-substituted
4,5-di-OMe ds1 isomer showed faster rates than the mono-
substituted 4-OMe (2.0-fold) and 5-OMe (1.5-fold) ds1
isomers. Conversely, both 5-OMe and 4,5-di-OMe ds2 isomers
exhibited the identical DT50 value of just 0.8 s. We note that in
the absence of an a substituent, Hasan et al. reported a rate
increase of only 1.2-fold for a 5-OMe-2-nitrobenzyl analogue
over its corresponding parent.[10b] Comparison of ds1 and ds2
isomers of dG.V.c with dG.V.a revealed higher rate increases
of 3.6-fold and 4.4-fold, respectively, suggesting that the
stereospecific tert-butyl group enhances the effect of the 5-
OMe group. With four-color CRT applications, this combina-
tion provides good flexibility for the utility of the ring system,
as a linker can be attached to the 4-position to create dye-
labeled analogues.[1a]
Table 1: Rates of photochemical cleavage for C7-HOMedA analogues.[a]
C7-HOMedA Analogue
DT50 in 1 mm NaN3
No DTT
50 mm DTT
dA.I
3.6Æ0.1
4.5Æ0.2
2.2Æ0.1
7.0Æ0.3
1.1Æ0.1
3.4Æ0.2
2.8Æ0.2
3.5Æ0.1
4.4Æ0.2
2.1Æ0.1
6.1Æ0.4
1.0Æ0.1
3.0Æ0.2
2.5Æ0.1
dA.III.a ds1
dA.III.a ds2
dA.III.b ds1
dA.III.b ds2
dA.III.c ds1
dA.III.c ds2
To determine the stereochemistry of these a-tert-butyl C7-
HOMedG analogues, the (1S)-camphanate of (R/S)-1-(5-
[a] A DT50 value is defined as the point in time at which 50% of the 2-
nitrobenzyl groups have been photochemically cleaved from the
extended primer/template complex. Lower DT50 values indicate faster
photochemical cleavage rates. DTT=dithiothreitol.
methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol
was
resolved into its enantiopure S alcohol by fractional crystal-
lization[11] (Figure S1 in the Supporting Information). This S
alcohol and (S)-a-tert-butyl-2-nitrobenzyl alcohol[3] were each
coupled to C7-HOMedG (Figure 1). RP-HPLC analysis of
their corresponding triphosphates revealed that both ds2
isomers of dG.V.a and dG.V.c have peak retention times
identical to those of dG.V and dG.VI, respectively, thus
indicating that both ds2 isomers have the same S configu-
ration at the a-carbon. By inference, the corresponding ds1
isomers of dG.V.a and dG.V.c have been assigned the R
configuration.
These S alcohols were then coupled to the remaining
nucleosides to examine the effect of the nucleotide leaving
group on the rate of photochemical cleavage. For example,
photochemical-cleavage experiments revealed that DT50
values for the parent 2-nitrobenzyl analogues ranged from
2.0 s for dC.I to 9.2 s for dG.I, suggesting that the leaving
group can influence the rate of photochemical cleavage
(Figure 2). Substitution of the benzylic carbon with a tert-
butyl group in the stereospecific S configuration, denoted
simply as (S)-a-tert-butyl, resulted in increased cleavage rates
by factors of 1.5–3.1, and the additional substitution with a 5-
rates (i.e., lower DT50 values) by factors of 2.0, 6.4, and 1.2,
respectively, compared to their ds1 counterparts. Interest-
ingly, the ds1 isomers exhibited similar (dA.III.c) or higher
(dA.III.a and dA.III.b) DT50 values than the parent dA.I.
These data provide evidence that the stereochemistry of the
a-substituted isopropyl group is an important determinant,
and coupled with a 4-OMe substitution, analogue dA.III.b ds2
produced the lowest DT50 value for the C7-HOMedA set.
Our previous work demonstrated that the a-tert-butyl
analogue dU.V exhibited excellent CRT properties, such as
single-base termination and high nucleotide selectivity.[3] This
allowed us to further examine the stereospecific effect using a
different a-substitution group coupled with various OMe ring
substitutions by synthesizing four a-tert-butyl C7-HOMedG
analogues, dG.V.a—dG.V.d, along with the parent dG.I
(Figure 1). Consistent with a-isopropyl-C7-HOMedATP ana-
logues, photochemical-cleavage experiments of the ds2 iso-
mers dG.V.a—dG.V.d showed faster rates by factors of 3.1,
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Figure 3. Elimination of transient product (TP) with DTT. Fluorescent
gel images of the photochemical cleavage of dU.VI incorporated by
Therminator polymerase in the presence of a) 1 mm NaN3 and
b) 1 mm NaN3, 50 mm DTT recorded at different times. Lanes: “P”
(primer) contains Therminator bound to oligoTemplate-4 hybridized
with BODIPY-FL-labeled primer-1 in 1x ThermoPol buffer,[3] “I” (incor-
poration) contains that found in lane “P” plus 100 nm dU.VI, and
time-point lanes contain that found in lane “I” plus exposure times to
0.70 WcmÀ2 365 nm light. “IP” denotes incorporated product and “CP”
denotes cleaved product.
Figure 2. Rates for the photochemical cleavage of the partent 2-nitro-
benzyl group as well as for the (S)-a-tert-butyl-, and (S)-a-tert-butyl-5-
OMe-modified 2-nitrobenzyl groups on C7-HOMedA, HOMedC, C7-
HOMedG, and HOMedU nucleosides. Nuc=nucleotide.
limited to just an a-tert-butyl group. We have shown several
examples of a-isopropyl ds2 isomers, presumed to have S
configuration, which also have faster rates for photochemical
cleavage than their ds1 isomers. In the presence of DTT, the
reactive nitrosoketone by-product can be eliminated effec-
tively during photochemical cleavage, creating appropriate
conditions to maintain the biological integrity of the CRT
reaction. We note that these 3’-OH-unblocked (S)-a-tert-
butyl-5-OMe-2-nitrobenzyl-modified nucleotides also exhibit
single-base termination, fast incorporation kinetics, and high
nucleotide selectivity (unpublished results). Thus, this work
not only expands the repertoire of 2-nitrobenzyl modifica-
tions that yield faster-cleaving protecting groups, but when
coupled with reversible terminators, yield faster cycle times
for NGS instrument systems.
OMe group further increased rates by factors of 3.0–11.5
compared with the parent analogues. The greatest rate
improvement was observed in the set of C7-HOMedG
analogues, for which DT50 values were reduced from 9.2 to
0.8 s (Figure 2, blue bars). The complete set of (S)-a-tert-
butyl-5-OMe reversible terminators showed a more narrow
range of DT50 values from 0.6 to 0.8 s. These data suggest that
the combined effects of the (S)-a-tert-butyl and 5-OMe
groups play an important role in diminishing the variation
in cleavage rates observed with particular nucleotide leaving
groups, which has the practical application of providing
normalized and faster cleavage conditions for the CRT cycle.
Following brief exposure to UV light, transient products
were observed from incorporation assays for (S)-a-tert-butyl-
5-OMe-C7-HOMedA, -HOMedC, and -HOMedU (Fig-
ure 3A), but not for -C7-HOMedG. As the only difference
was the just-incorporated nucleotide, we hypothesize that the
faster cleaving (S)-a-tert-butyl-5-OMe-2-nitrobenzyl group
produces a more reactive 2-nitrosoketone by-product, which
attacks the 3’-terminal nucleotide of the growing primer
strand. To investigate conditions for quenching the nitroso
intermediate, a number of amino and thiol agents were tested
(Figure S2 in the Supporting Information). Of these, only
dithiothreitol (DTT)[12] eliminated the transient product
(Figure 3B). To test rate effects, photochemical-cleavage
experiments were repeated for all compounds in the presence
of DTT, of which DT50 values for several parent and ds1
isomers were reduced (Tables 1 and 2, and Table S3). Corrie
and colleagues proposed that DTT attacks the nitroso group
by nucleophilic addition,[13] thereby, providing in our case
protection against such undesired reactions.
Received: September 14, 2011
Published online: January 9, 2012
Keywords: cleavage reactions · nucleotides · photochemistry ·
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reversible terminators
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