6 research outputs found
Synthesis and Nonenzymatic Template-Directed Polymerization of 2′-Amino-2′-deoxythreose Nucleotides
Threose nucleic acid (TNA) is a potential
alternative genetic material
that may have played a role in the early evolution of life. We have
developed a novel synthesis of 2′-amino modified TNA nucleosides
(2′-NH<sub>2</sub>-TNA) based on a cycloaddition reaction between
a glycal and an azodicarboxylate, followed by direct nucleosidation
of the cycloadduct. Using this route, we synthesized the thymine and
guanine 2′-NH<sub>2</sub>-TNA nucleosides in seven steps with
24% and 12% overall yield, respectively. We then phosphorylated the
guanine nucleoside on the 3′-hydroxyl, activated the phosphate
as the 2-methylimidazolide, and tested the ability of the activated
nucleotide to copy C<sub>4</sub> RNA, DNA, and TNA templates by nonenzymatic
primer extension. We measured pseudo-first-order rate constants for
the first nucleotide addition step of 1.5, 0.97, and 0.57 h<sup>–1</sup> on RNA, DNA, and TNA templates, respectively, at pH 7.5 and 4 °C
with 150 mM NaCl, 100 mM <i>N</i>-(hydroxylethyl)Âimidazole
catalyst, and 5 mM activated nucleotide. The activated nucleotide
hydrolyzed with a rate constant of 0.39 h<sup>–1</sup>, causing
the polymerization reaction to stall before complete template copying
could be achieved. These extension rates are more than 1 order of
magnitude slower than those for amino-sugar ribonucleotides under
the same conditions, and copying of the TNA template, which best represented
a true self-copying reaction, was the slowest of all. The poor kinetics
of 2′-NH<sub>2</sub>-TNA template copying could give insight
into why TNA was ultimately not used as a genetic material by biological
systems
Synthesis and Nonenzymatic Template-Directed Polymerization of 2′-Amino-2′-deoxythreose Nucleotides
Threose nucleic acid (TNA) is a potential
alternative genetic material
that may have played a role in the early evolution of life. We have
developed a novel synthesis of 2′-amino modified TNA nucleosides
(2′-NH<sub>2</sub>-TNA) based on a cycloaddition reaction between
a glycal and an azodicarboxylate, followed by direct nucleosidation
of the cycloadduct. Using this route, we synthesized the thymine and
guanine 2′-NH<sub>2</sub>-TNA nucleosides in seven steps with
24% and 12% overall yield, respectively. We then phosphorylated the
guanine nucleoside on the 3′-hydroxyl, activated the phosphate
as the 2-methylimidazolide, and tested the ability of the activated
nucleotide to copy C<sub>4</sub> RNA, DNA, and TNA templates by nonenzymatic
primer extension. We measured pseudo-first-order rate constants for
the first nucleotide addition step of 1.5, 0.97, and 0.57 h<sup>–1</sup> on RNA, DNA, and TNA templates, respectively, at pH 7.5 and 4 °C
with 150 mM NaCl, 100 mM <i>N</i>-(hydroxylethyl)Âimidazole
catalyst, and 5 mM activated nucleotide. The activated nucleotide
hydrolyzed with a rate constant of 0.39 h<sup>–1</sup>, causing
the polymerization reaction to stall before complete template copying
could be achieved. These extension rates are more than 1 order of
magnitude slower than those for amino-sugar ribonucleotides under
the same conditions, and copying of the TNA template, which best represented
a true self-copying reaction, was the slowest of all. The poor kinetics
of 2′-NH<sub>2</sub>-TNA template copying could give insight
into why TNA was ultimately not used as a genetic material by biological
systems
Synthesis and Nonenzymatic Template-Directed Polymerization of 2′-Amino-2′-deoxythreose Nucleotides
Threose nucleic acid (TNA) is a potential
alternative genetic material
that may have played a role in the early evolution of life. We have
developed a novel synthesis of 2′-amino modified TNA nucleosides
(2′-NH<sub>2</sub>-TNA) based on a cycloaddition reaction between
a glycal and an azodicarboxylate, followed by direct nucleosidation
of the cycloadduct. Using this route, we synthesized the thymine and
guanine 2′-NH<sub>2</sub>-TNA nucleosides in seven steps with
24% and 12% overall yield, respectively. We then phosphorylated the
guanine nucleoside on the 3′-hydroxyl, activated the phosphate
as the 2-methylimidazolide, and tested the ability of the activated
nucleotide to copy C<sub>4</sub> RNA, DNA, and TNA templates by nonenzymatic
primer extension. We measured pseudo-first-order rate constants for
the first nucleotide addition step of 1.5, 0.97, and 0.57 h<sup>–1</sup> on RNA, DNA, and TNA templates, respectively, at pH 7.5 and 4 °C
with 150 mM NaCl, 100 mM <i>N</i>-(hydroxylethyl)Âimidazole
catalyst, and 5 mM activated nucleotide. The activated nucleotide
hydrolyzed with a rate constant of 0.39 h<sup>–1</sup>, causing
the polymerization reaction to stall before complete template copying
could be achieved. These extension rates are more than 1 order of
magnitude slower than those for amino-sugar ribonucleotides under
the same conditions, and copying of the TNA template, which best represented
a true self-copying reaction, was the slowest of all. The poor kinetics
of 2′-NH<sub>2</sub>-TNA template copying could give insight
into why TNA was ultimately not used as a genetic material by biological
systems
Efficient and Rapid Template-Directed Nucleic Acid Copying Using 2′-Amino-2′,3′-dideoxyribonucleoside−5′-Phosphorimidazolide Monomers
The development of a sequence-general nucleic acid copying system is an essential step in the assembly of a synthetic protocell, an autonomously replicating spatially localized chemical system capable of spontaneous Darwinian evolution. Previously described nonenzymatic template-copying experiments have validated the concept of nonenzymatic replication, but have not yet achieved robust, sequence-general polynucleotide replication. The 5′-phosphorimidazolides of the 2′-amino-2′,3′-dideoxyribonucleotides are attractive as potential monomers for such a system because they polymerize by forming 2′→5′ linkages, which are favored in nonenzymatic polymerization reactions using similarly activated ribonucleotides on RNA templates. Furthermore, the 5′-activated 2′-amino nucleotides do not cyclize. We recently described the rapid and efficient nonenzymatic copying of a DNA homopolymer template (dC<sub>15</sub>) encapsulated within fatty acid vesicles using 2′-amino-2′,3′-dideoxyguanosine−5′-phosphorimidazolide as the activated monomer. However, to realize a true Darwinian system, the template-copying chemistry must be able to copy most sequences and their complements to allow for the transmission of information from generation to generation. Here, we describe the copying of a series of nucleic acid templates using 2′-amino-2′,3′-dideoxynucleotide−5′-phosphorimidazolides. Polymerization reactions proceed rapidly to completion on short homopolymer RNA and LNA templates, which favor an A-type duplex geometry. We show that more efficiently copied sequences are generated by replacing the adenine nucleobase with diaminopurine, and uracil with C5-(1-propynyl)uracil. Finally, we explore the copying of longer, mixed-sequence RNA templates to assess the sequence-general copying ability of 2′-amino-2′,3′-dideoxynucleoside−5′-phosphorimidazolides. Our results are a significant step forward in the realization of a self-replicating genetic polymer compatible with protocell template copying and suggest that N2′→P5′-phosphoramidate DNA may have the potential to function as a self-replicating system
Crystal Structure Studies of RNA Duplexes Containing s<sup>2</sup>U:A and s<sup>2</sup>U:U Base Pairs
Structural studies of modified nucleobases
in RNA duplexes are
critical for developing a full understanding of the stability and
specificity of RNA base pairing. 2-Thio-uridine (s<sup>2</sup>U) is
a modified nucleobase found in certain tRNAs. Thermodynamic studies
have evaluated the effects of s<sup>2</sup>U on base pairing in RNA,
where it has been shown to stabilize U:A pairs and destabilize U:G
wobble pairs. Surprisingly, no high-resolution crystal structures
of s<sup>2</sup>U-containing RNA duplexes have yet been reported.
We present here two high-resolution crystal structures of heptamer
RNA duplexes (5′-uagc<b><u>s</u></b><sup><b><u>2</u></b></sup><b><u>U</u></b>cc-3′ paired with 3′-aucg<b><u>A</u></b>gg-5′ and with 3′-aucg<b><u>U</u></b>gg-5′) containing s<sup>2</sup>U:A and s<sup>2</sup>U:U pairs, respectively. For comparison, we also present the structures
of their native counterparts solved under identical conditions. We
found that replacing O2 with S2 stabilizes the U:A base pair without
any detectable structural perturbation. In contrast, an s<sup>2</sup>U:U base pair is strongly stabilized in one specific U:U pairing
conformation out of four observed for the native U:U base pair. This
s<sup>2</sup>U:U stabilization appears to be due at least in part
to an unexpected sulfur-mediated hydrogen bond. This work provides
additional insights into the effects of 2-thio-uridine on RNA base
pairing
Bidirectional Direct Sequencing of Noncanonical RNA by Two-Dimensional Analysis of Mass Chromatograms
Mass
spectrometry (MS) is a powerful technique for characterizing
noncanonical nucleobases and other chemical modifications in small
RNAs, yielding rich chemical information that is complementary to
high-throughput indirect sequencing. However, mass spectra are often
prohibitively complex when fragment ions are analyzed following either
solution phase hydrolysis or gas phase fragmentation. For all but
the simplest cases, ions arising from multiple fragmentation events,
alternative fragmentation pathways, and diverse salt adducts frequently
obscure desired single-cut fragment ions. Here we show that it is
possible to take advantage of predictable regularities in liquid chromatographic
(LC) separation of optimized RNA digests to greatly simplify the interpretation
of complex MS data. A two-dimensional analysis of extracted compound
chromatograms permits straightforward and robust de novo sequencing,
using a novel Monte Carlo algorithm that automatically generates bidirectional
paired-end reads, pinpointing the position of modified nucleotides
in a sequence. We demonstrate that these advances permit routine LC–MS
sequencing of RNAs containing noncanonical nucleotides, and we furthermore
examine the applicability of this approach to the study of oligonucleotides
containing artificial modifications as well as those commonly observed
in post-transcriptionally modified RNAs