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J. Biol. Chem., Vol. 275, Issue 37, 28984-28988, September 15, 2000
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,From the Unité de Génétique et Biochimie du Développement, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
Received for publication, June 23, 2000
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ABSTRACT |
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Terminal deoxynucleotidyltransferase (TdT)
catalyzes the addition of nucleotides to 3'-hydroxyl ends of DNA
strands in a template-independent manner and has been shown to add
N-regions to gene segment junctions during V(D)J recombination. TdT is
highly conserved in all vertebrate species, with a second isoform,
characterized by a 20-amino acid insertion near the COOH-terminal end,
described only in the mouse. The two murine isoforms differ in their
subcellular localization, and the long isoform (TdTL) has previously
been found to be unable to add N-regions. Using purified protein
produced in a high level expression system in Escherichia
coli, we were able to carry out detailed catalytic comparisons of
these two TdT isoforms. We discovered that TdTL exhibits terminal
transferase activity with kinetic parameters similar to those of the
conserved TdT isoform (TdTS). We observed, however, that TdTL is
inactivated at physiologic temperature but stable at lower
temperatures. This thermal sensitivity of TdTL polymerase activity is
not correlated with a significant change in the circular dichroism
spectrum of the protein. Thus, the 20-amino acid insertion in TdTL does
not affect the catalytic activity but modifies the thermosensitivity.
Terminal deoxynucleotidyltransferase
(TdT,1 EC 2.7.7.31) is
the only known enzyme to catalyze the
nontemplated addition of nucleotides to 3'-hydroxyl ends of DNA strands
(1). This polymerase function has an important role in the
diversification of the immunoglobulin and T cell receptor repertoires
in vertebrates, enabling TdT to add random nucleotides, called
N-regions, to the junctions of gene segments during V(D)J recombination
(2, 3). TdT is highly conserved across the vertebrate phylum, from bony
fish to man (4-8), yet the mouse is the only species in which two TdT
isoforms have been discovered. Analysis of a mouse genetic clone
containing the 3'-region of the TdT gene revealed the presence of an
additional exon (exon X-bis). We identified two alternatively spliced
TdT mRNAs in mouse bone marrow and thymus. The longer TdT mRNA
has an insertion of 60 nucleotides encoded by the additional exon near
the carboxyl-terminal end of the gene and codes for a protein of 529 amino acids (TdTL). The shorter mRNA codes for a protein of 509 amino acids (TdTS) (9). Catalytic and functional differences between
the short and the long murine TdT isoforms have been described but not
explained. We have previously shown, in transfection experiments using
either fibroblasts or COS cells, that TdTS and TdTL differ in their
subcellular localization and their ability to add N-regions to V(D)J
junctions during recombination of an episomic substrate. In this
system, TdTS is strictly nuclear and adds N-nucleotides at V(D)J
junctions, whereas TdTL is essentially cytoplasmic and does not add
N-nucleotides. Comparison of terminal transferase activity in extracts
of TdTS and TdTL transfected cells led to the hypothesis that the
inability of TdTL to add N-regions could be due to a defective
polymerase activity (10).
The lack of an adequate, unproteolysed protein source has been a
constraint on research on TdT. We have recently developed a method of
production and purification of TdT in Escherichia coli (11),
allowing us to carry out extensive kinetics and structural analyses of
the protein. Here we report for the first time that TdTL displays the
same terminal transferase activity as TdTS but that the 20-amino acid
insertion conveys heat sensitivity.
Purification of the Two Murine TdT Isoforms--
The protocol
used for expression and purification of recombinant TdTS has been
described (11). It was modified for the expression and purification of
TdTL, since the protein was recovered in inclusion bodies when the
cells were grown at 15 °C and was poorly retained on the nickel
affinity column at high stringency. Cells transformed with the
TdTL expression vector were grown at 25 °C until OD600 reached 0.8. After addition of 1 mM IPTG, cultures
were incubated at 10 °C during 24-36 h. Cells were harvested by
centrifugation at 2600 g for 15 min, resuspended in 0.05 volume of buffer AL (10 mM Tris-HCl, pH 8.0, 0.25 M NaCl), and lysed in a French press at 16,000 p.s.i.
The lysate was cleared by centrifugation for 30 min at 20,000 × g. The supernatant was then sonicated, filtered through a
0.45-µm filter, and loaded at a rate of 1 ml/min on a 5-ml Hitrap
affinity column (Amersham Pharmacia Biotech, Uppsala, Sweden)
charged with Ni2+ ions and equilibrated with buffer
AL. The column was washed with 3 volumes of buffer
AL, 100 mM imidazole, and TdTL was
eluted with a gradient of 100-300 mM imidazole on a FPLC
system (Amersham Pharmacia Biotech) at a rate of 2 ml/min. The purest
fractions were pooled and dialyzed against buffer B (50 mM
Hepes, pH 7.0, 50 mM MgOAc, 50 mM
(NH4)2SO4, 200 mM NaCl). Dialyzed
fractions were concentrated with microsep 10K centrifugal concentrator
(Pall Filtron, Northborough, MA) and stored at TdT Enzymatic Assays and Determination of Kinetic
Parameters--
Two substrates are involved in the terminal
transferase nucleotidyl transfer reaction: a single stranded DNA
(initiator) and a deoxynucleoside triphosphate. Michaelis-Menten
kinetic parameters (KmdATP,
Km(dA)10, and
kcat) were obtained by titrating each substrate
in the presence of a saturating concentration of a second substrate, as
described previously (11). (dA)10 and (dA)50
oligonucleotide primers were purchased from Genset (Paris, France).
Ultrapure deoxyribonucleotide solutions were purchased from Amersham
Pharmacia Biotech (Uppsala, Sweden).
Terminal transferase activity was detected by incorporation of dATP
into single-stranded DNA using the following standard assay:
recombinant proteins were incubated at 35 °C in 200 mM potassium cacodylate, 25 mM Tris-HCl, pH 6.6, 0.25 mg/ml
bovine serum albumin, 4 mM MgCl2, 4 µM ZnSO4, 1 mM
[
Owing to the distributive mechanism of TdT polymerization, analysis of
chain length distribution was done at low oligonucleotide primer
concentration. 5 µM 5'-32P-labeled
(dA)10 primer was used as the radioactive substrate. Aliquots were withdrawn at different times, supplemented with a
formamide dye mix (10 mM NaOH, 95% formamide, 0.05%
bromphenol blue, 0.05% xylene cyanole), and electrophoresed, after
heat denaturation, on a 16% acrylamide denaturing gel. TdT products
were visualized after exposure of the wet gel under a Kodak film
(Biomax MR) at Thermostability--
To measure the thermostability of TdT
isoforms, proteins at 3 µM in the storage buffer (25 mM Hepes, pH 7.0, 25 mM MgOAc, 25 mM (NH4)2SO4, and 100 mM NaCl, 50% glycerol) were preincubated at various
temperatures ranging from 20 to 60 °C for 10 min or at 35 °C for
various times and chilled on ice. The residual activity was measured at
35 °C in the standard kinetic assay buffer with 100 µM
(dA)10, 1 mM [ Circular Dichroism (CD) Spectrum--
Secondary structures of
recombinant proteins were measured using circular dichroism on a
Jobin-Yvon CD6 spectrometer (Longjumeau, France). Measurements were
done at wavelengths from 195 to 260 nm, at two temperatures. First
measurement was done at 25 °C. The temperature was then raised
progressively to 35 °C and proteins incubated further for 20 min,
before the second measurement was done. For each temperature three
independent measurements were performed. Concentrations of protein
solutions were 1 mg/ml in 2× storage buffer without glycerol.
The 20-Amino Acid Insertion in the Long Isoform of Murine TdT Is
Localized in the Highly Conserved Carboxyl-terminal Region--
A
multiple alignment of all known TdT sequences was drawn using the
Pileup program (Genetics Computer Group version 9.0), and a
consensus sequence was deduced (Fig. 1).
153 amino acids are shared by all the sequences analyzed, corresponding
to 30% identity, and 71 amino acids are functionally equivalent,
leading to an overall similarity of 44%. TdT protein can be divided
into three regions: the NH2-terminal domain, which is
dispensable for TdT activity
(13),2 and the so-called TdTL Is a True Terminal Deoxynucleotidyltransferase--
Catalytic
activities of purified TdTS and TdTL were measured using a standard
assay (described under "Experimental Procedures") with dATP and
(dA)10 as substrates. Initial velocities (Vi)
were determined using linear regression on appropriate time courses (every 30 s for 3.5 min) and were normalized to the concentration of TdT. For both TdTS and TdTL, we observed a hyperbolic dependence of
initial rates on the concentration of the varying substrates (data not
shown). Michaelis-Menten kinetic parameters were obtained using the
Kaleidagraph program (Synergy Software, FCF Inc., Reading PA) and are
presented in Table I. There is
only a 2-fold reduction in TdTL specific activity as compared with
TdTS. TdTL has the same apparent affinity for dATP, a higher apparent
affinity for (dA)10 (over 2-fold), and a somewhat lower
polymerization rate (about 2-3-fold difference in
kcat for dATP and (dA)10). Thus, TdTL has true terminal transferase activity with kinetic parameters similar to those of TdTS.
Thermosensitivity of TdTL Catalytic Activity--
When we compared
the behavior of the two proteins over a long time course in our
standard assay we noticed that TdTL quickly reached a plateau. Less
than 10% (about 5.0 nmol) of the initial dATP could be incorporated,
whereas TdTS was capable of consuming, in an hour, 80% (40 nmol) of
the total amount of dATP present in the reaction (Fig.
2A). The chain length
distributions at low (dA)10 concentration (5 µM) also reflected the differences between the two
isoforms. TdTS synthesized much longer products than TdTL. The size of
the TdTS products grew over time, whereas the size distribution of the
TdTL products remained uniform (Fig. 2B). The same
differences in the TdTS and TdTL chain length distribution patterns
were observed in the presence of the four deoxyribonucleotides (Fig.
2C). One hypothesis for the distinctive behavior of TdTL could be the inability of the protein to extend longer DNA chains. We
thus measured the catalytic activity of TdTL on a (dA)50
oligonucleotide primer. (dA)50 was elongated efficiently,
and a plateau of incorporation was again observed after 20 min of
incubation (data not shown). Alternatively, the plateau could reflect a
lack of stability and, thus, an inactivation of the protein in the
reaction conditions. The residual activity of the two TdT isoforms was
measured at 35 °C after preincubation for 10 min at varying
temperatures from 20 to 60 °C. The reactions were started upon the
addition of the enzyme and initial velocities were measured. The
temperature inactivation curves are shown in Fig.
3A. The inflection point
occurred at 37 °C for TdTL and at 45 °C for TdTS. This result
suggested that TdTL was indeed unstable around the temperature
(35 °C) commonly used. This was further confirmed by measuring the
enzymes residual activities after preincubation at 35° over varying
periods of time from 15 to 60 min. As can be seen in Fig.
3B, the residual activity was 60% for TdTS but only 20%
for TdTL after 60 min of preincubation at 35 °C. We verified, using
SDS-polyacrylamide gel electrophoresis analysis, that there was no
apparent protein degradation even after an hour of incubation at
35 °C. Furthermore, addition to the reaction buffer of bacterial
protease inhibitors did not prevent the inactivation of TdTL (data not
shown). These observations led us to assess the retention of secondary
structures of the two proteins by comparing their CD spectra. The
analyses were first done at 25 °C, where both isoforms are stable.
At this temperature, TdTS and TdTL CD spectra were similar with a mean molar ellipticity at 210 nm around
To test the possibility that the two isoforms could interact in
vitro and exert an influence on each other, we compared the activity of a mixture of the two enzymes to the activity of each enzyme
tested separately. As can be seen in Fig.
5, with a standard kinetic assay for
incorporation of TdT has attracted great interest because of its unique catalytic
capability, role in V(D)J recombination, unexplained evolutionary lineage, and numerous applications in molecular biology. We have previously demonstrated the presence of two TdT isoforms in the mouse,
both expressed in the thymus and bone marrow (9). Our initial attempts
to compare the activities of the two murine TdT isoforms were carried
out with extracts of TdTS or TdTL transfected cells, where the proteins
were poorly expressed and labile (10). To overcome these problems, we
recently developed a method of production of murine TdT in E. coli by which large amounts of purified, unproteolysed TdTS are
easily obtained (11). Since the presence of the 20-amino acid insertion
modifies the biochemical properties of the protein, certain minor
modifications in the expression and purification steps were required to
optimize the recovery of TdTL.
Both recombinant short and long TdT isoforms exhibit terminal
transferase activity, with similar kinetic parameters. They are both
capable of polymerizing long chains of single-stranded DNA, but a
plateau of incorporation of deoxynucleotides is always observed
with TdTL after a short period of incubation at standard temperature.
Our analysis of heat-induced denaturation of the two TdT isoforms
argues for a correlation between the plateau and the thermal
instability of TdTL. The TdT active site, as inferred from
sequence alignments, cross-linking (20), and mutagenesis experiments
(19),2 contains a constellation of amino acids from
both Temperature sensitivity acquired by spontaneous mutations has been
described for several proteins. A defect in the cellular trafficking of
thermosensitive mutants of human tyrosinase and cystic fibrosis
transmembrane conductance regulator has been correlated with a
loss of activity in vivo (21, 22). It remains to be determined whether cultivating transfected cells at lower temperatures can modify the subcellular localization of TdTL and rescue its putative
cellular function. The possibility that TdTL in vivo plays a
role distinct from N-nucleotide addition will need to be explored.
TdT has only been found in vertebrates and no homolog to murine TdTL
has been reported. Genomic data are yet to be collected to allow the
search for an exon homologous to the murine TdT exon X-bis. Murine TdTL
could represent an ancestral, perhaps vestigial, form of the
enzyme (23) or may result from an evolutionary happenstance, such as
the late capture of an additional exon. The evolutionary origin of TdT
is a matter of interest and debate. Based upon some sequence similarity
with polymerase
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INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
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EXPERIMENTAL PROCEDURES
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
80 °C after
addition of 50% glycerol. Purified proteins were analyzed by
SDS-polyacrylamide gel electrophoresis, using an 8% acrylamide
gel. Gels were stained with Coomassie Blue or probed with polyclonal
rabbit anti-bovine TdT serum (a generous gift from F. J. Bollum).
No degradation products were detected on the Western blot.
Densitometric analysis with a MasterScan I Interpretive densitometer
(Scananalytics) of the Coomassie-stained gel led to an estimation of
the purity of the two proteins superior to 80%. Protein concentration
was calculated using a theoretical extinction coefficient of 54,870 M
1 cm
1 (12).
-32P]dATP (70 cpm/pmol), and 100 µM
oligonucleotide primer unless otherwise specified. Reactions were
stopped at different times with 15 mM EDTA. Aliquots were
spotted onto Whatman DE81 discs. Unpolymerized nucleotides were washed
away by immersing the discs three times for 5 min in
NH4COOH/Na4P2O7·10H2O
(300 mM/10 mM) and then in H2O and
in EtOH. Dried discs were counted in a scintillation fluid (Econofluor
from Packard, Göningen, The Netherlands). Kinetic curves show the
percentage of total dATP present in the reaction incorporated over time.
70 °C.
-32P]dATP at 70 cpm/pmol, and 200 nM TdTS or TdTL.
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RESULTS
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
and
peptides (14). Positions are given for the murine TdTS. The
NH2-terminal region (aa 1-131, 37% similarity) contains a
consensus nuclear localization sequence (aa 11-17) (13) and a
conserved BRCA1 carboxyl terminus-like sequence (aa 27-124),
which is a protein-protein interaction domain first identified in the
COOH-terminal region of the BRCA1 breast cancer suppressor protein (15)
and later in many other proteins, including some involved in DNA damage
repair and recombination (16, 17). It was recently demonstrated that,
in vitro, this domain in TdT interacts with the Ku70/86
heterodimer that binds DNA and is involved in double-strand break
repair and V(D)J recombination (18). Mutagenesis experiments of
human TdT showed that two amino acids analogous to
Asp343 and Asp345 in murine TdT are
essential for catalysis (19). We have shown that Asp434 is
also required for catalysis.2 The catalytic center
of the protein thus contains amino acids from both
peptide (aa
132-421, 41% similarity) and
peptide (aa 422-510, 67%
similarity). The 20-amino acid insertion is located at position 482 in
the
peptide, which is the most conserved region in all the analyzed
sequences (46% identity).

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Fig. 1.
Alignment of TdT amino acid
sequences. An amino acid sequence alignment of the two murine TdT
isoforms with seven other vertebrate TdT was drawn using the Pileup
program (Genetics Computer Group version 9.0), and a consensus
sequence was deduced manually. Functionally equivalent amino acids were
considered as follows: Leu, Ile, Met, and Val; Ala and G; Tyr, Trp, and
Phe; Asp, Glu, Gln, and Asn; Lys, Arg, and His; Ser and Thr and
are shown in italics. Strictly conserved amino acids are in
plain text. Strictly conserved aspartate residues involved in catalysis
(Asp343, Asp345, Asp434) are
underlined in the consensus sequence. In the murine TdTS
sequence, the
peptide comprises amino acids 131-421 and the
peptide amino acids 422-510. Accession numbers in the Swiss Protein
Data Bank are as follows: mouse, P09838; cattle, P06526; human,
P04053; opossum, O02789; chicken, P36195; Xenopus, P42118;
axolotl, O57486; and rainbow trout, Q92089.
Kinetic parameters of TdTS and TdTL
15,000 degree·cm2
dmol
1. This low value reflects the
abundance of
-helices and
-sheets. The proteins were then slowly
brought to 35 °C and further incubated for 20 min at this
temperature. Both isoforms retained a low molar ellipticity (Fig.
4). The thermosensitivity of TdTL
catalytic activity is thus not correlated with a loss of secondary
structure.

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Fig. 2.
Terminal transferase activity of TdTS and
TdTL. 250 nM TdTS (closed circles) or TdTL
(closed squares) were incubated with 1 mM
-32P-labeled dATP and 100 µM
(dA)10. The percentage of total dATP incorporated was
measured at 0, 5, 7.5, 10, 15, 30, and 60 min (A). Each
experiment was repeated several times, and results were averaged.
Error bars represent the S.D. Reaction conditions for
analysis of chain length distribution were as described above, except
that (dA)10 was the 32P-labeled substrate (5 µM). Reactions were carried out with 1 mM
dATP (B) or with 250 µM of each nucleotide
(dATP, dTTP, dGTP, dCTP) (C). Aliquots of the reactions
taken at 0, 10, 15, 30, and 60 min were analyzed on a 16%
polyacrylamide denaturing gel.

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Fig. 3.
Thermosensitivity of TdTS and TdTL.
Concentrated enzyme solutions (3 µM) were incubated at
various temperatures for 10 min (A) or at 35 °C for the
time indicated (B). The residual activity was measured by
incorporation of
-32P-labeled dATP on a
(dA)10 primer in our standard enzymatic assay at 35 °C
and is expressed as a percentage of the original activity without
preincubation. Reactions were carried out with 1 mM
nucleotides and 200 nM TdTS (black circles) or
TdTL (black squares). Each experiment was repeated several
times and results were averaged. Error bars represent the
S.D.

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Fig. 4.
Retention of secondary structures by TdTS and
TdTL. Circular dichroism spectra of TdTS and TdTL were measured at
wavelengths from 195 to 260 nm, at 25 °C (solid line) and
35 °C (dashed line), as described under "Experimental
Procedures." The curves represent the mean of three independent
measurements. The mean molar ellipticity [
] was calculated with
the formula: [
] = (MRW)(
)/(10 × L × C), where MRW is the molar residue weight in dalton,
the
circular dichroism value in millidegrees, L the path
length (0.1 cm), and C the concentration of the enzyme (1 mg/ml).
-32P-labeled dATP on a
(dA)10 primer, the activities of TdTS and TdTL were
additive. The same result was obtained when the experiment was carried
out with different ratios of the two enzymes (data not shown).

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Fig. 5.
Activity of TdTS and TdTL mixture.
Terminal transferase activity was measured by incorporation of
-32P-labeled dATP on a (dA)10 primer in our
standard enzymatic assay. Reactions were carried out with 290 nM TdTS (black circles), 290 nM TdTL
(black squares), or 290 nM amounts of
each enzyme (black triangles). The percentage of total dATP
incorporated was measured between 0 and 40 min. The curve corresponding
to the addition of the dATP incorporated by TdTS and TdTL tested in
separate assays is also displayed (open triangles). Each
experiment was repeated several times, and results were averaged.
Error bars represent the S.D.
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DISCUSSION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
and
peptides. Interestingly, the 20-amino acid insertion
in the long murine TdT isoform is located near the COOH-terminal end of
the protein, in the region that is the most conserved in all the TdT
sequences analyzed. It is conceivable that the 20-amino acid insertion
destabilizes the tertiary structure of the protein and affects
the geometry of the active site at higher temperatures, precluding the
interactions with substrates, nucleotides, and/or primer. These changes
must be subtle, since the thermosensitivity of TdTL polymerase activity is not correlated with a loss of secondary structures, as inferred from
analyses of the CD spectrum. The possibility of an interaction between
TdTS and TdTL in vitro was considered. Kinetic analysis of a
mixture of the two TdT isoforms indicates that TdTL does not inhibit
the activity of TdTS. Furthermore, if the rapid loss of activity were
due to a contaminant in the TdTL preparation, such as a protease, we
would have expected to observe an effect of the mixing on TdTS
stability as well. Such was not the case, thus arguing instead for an
intrinsic instability of the long isoform at physiologic temperature.
, TdT has been classified in the family X
polymerases (24), a subclass of an ancient
nucleotidyltransferase superfamily whose members share a common
signature in the active site and catalyze the same chemical reaction
but have diverse biological roles (25, 26). Confirmation of this
filiation awaits the elucidation of TdT tertiary structure.
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ACKNOWLEDGEMENTS |
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We thank Dr. Alain Chaffotte for help in the determination of the circular dichroism spectra.
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FOOTNOTES |
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* The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
C. P. dedicates her contribution to this work to the memory of Dr. Philippe Jérôme Lecomte deceased in Paris on January 18, 2000.
Supported by a fellowship from the Ministère de l'Education
Nationale de la Recherche et de la Technologie.
§ To whom correspondence should be addressed. Tel.: 33-1-40-61-34-44; Fax: 33-1-40-61-34-40; E-mail: papanico@pasteur.fr.
Published, JBC Papers in Press, June 30, 2000, DOI 10.1074/jbc.M005544200
2 J. B. Boulé, F. Rougeon, and C. Papanicolaou, unpublished result.
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ABBREVIATIONS |
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The abbreviations used are: TdT, terminal deoxynucleotidyltransferase; aa, amino acids.
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REFERENCES |
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