Thermodynamic Analysis of Duplex Formation of the Heterochiral DNA with l-Deoxyadenosine

Kawakami, Junji; Tsujita, Kazuhiko; Sugimoto, Naoki

doi:10.2116/analsci.21.77

Cited by 12 publications

(2 citation statements)

References 43 publications

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“…It has been reported that nucleotide selection by DNA polymerases are influenced by base stacking, Watson–Crick hydrogen bonding, and steric interactions, which are strong contributors to the overall stabilization of the double helix. The stability of DNA duplex is not only important but also essential to efficient and highly selective replication. , The heterochiral DNAs that contain an l -nucleoside within natural d sequences are found to retain the B-form duplex structure when hybridized with complementary homochiral d -sequences, − and l -nucleosides can locate their bases for Watson–Crick base pairing with natural nucleic acids. , Chiral modification decreases the duplex stability of heterochiral oligodeoxynucleotides containing an l -nucleoside within natural sequences (Δ T m = 5.5 °C, Figure S13), narrowing the gap of stability between a mismatching base pair and a matching base pair, so that the base-pairing selectivity may be lower with l -nucleotide in heterochiral duplexes than their corresponding homochiral duplexes . These observations are highly suggestive of the miscoding potential of l -T in the template during DNA replication.…”

Section: Resultsmentioning

confidence: 99%

Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases

et al. 2017

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DNA polymerases are known to recognize preferably d-nucleotides over l-nucleotides during DNA synthesis. Here, we report that several general DNA polymerases catalyze polymerization reactions of nucleotides directed by the DNA template containing an l-thymidine (l-T). The results display that the 5'-3' primer extension of natural nucleotides get to the end at chiral modification site with Taq and Phanta Max DNA polymerases, but the primer extension proceeds to the end of the template catalyzed by Deep Vent (exo), Vent (exo), and Therminator DNA polymerases. Furthermore, templating l-nucleoside displays a lag in the deoxyribonucleotide triphosphate (dNTP) incorporation rates relative to natural template by kinetics analysis, and polymerase chain reactions were inhibited with the DNA template containing two or three consecutive l-Ts. Most interestingly, no single base mutation or mismatch mixture corresponding to the location of l-T in the template was found, which is physiologically significant because they provide a theoretical basis on the involvement of DNA polymerase in the effective repair of l-T that may lead to cytotoxicity.

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Section: Resultsmentioning

confidence: 99%

Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases

et al. 2017

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“…and Kawakami et al . studied the influence of single L-nucleotide residue on the stability of DNA, RNA and DNA/RNA duplexes and demonstrated that the incorporation of an unnatural residue significantly destabilizes formed structures [ 21 – 23 ].…”

Section: Introductionmentioning

confidence: 99%

Thermodynamic Features of Structural Motifs Formed by β-L-RNA

et al. 2016

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This is the first report to provide comprehensive thermodynamic and structural data concerning duplex, hairpin, quadruplex and i-motif structures in β-L-RNA series. Herein we confirm that, within the limits of experimental error, the thermodynamic stability of enantiomeric structural motifs is the same as that of naturally occurring D-RNA counterparts. In addition, formation of D-RNA/L-RNA heterochiral duplexes is also observed; however, their thermodynamic stability is significantly reduced in reference to homochiral D-RNA duplexes. The presence of three locked nucleic acid (LNA) residues within the D-RNA strand diminishes the negative effect of the enantiomeric, complementary L-RNA strand in the formation of heterochiral RNA duplexes. Similar behavior is also observed for heterochiral LNA-2′-O-methyl-D-RNA/L-RNA duplexes. The formation of heterochiral duplexes was confirmed by 1H NMR spectroscopy. The CD curves of homochiral L-RNA structural motifs are always reversed, whereas CD curves of heterochiral duplexes present individual features dependent on the composition of chiral strands.

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Anomeric and Enantiomeric 2’‐Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions

Zhang

Budow-Busse

Leonard

et al. 2021

Chemistry A European J

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Dodecamer duplex DNA containing anomeric (α/ β-d) and enantiomeric (β-l/β-d) 2'-deoxycytidine mismatches was studied with respect to base pair stability in the absence and presence of silver ions. Stable duplexes with silver-mediated cytosine-cytosine pairs were formed by all anomeric and enantiomeric combinations. Stability changes were observed depending on the composition of the mismatches. Most strikingly, the new silver-mediated base pair of anomeric α-d-dC with enantiomeric β-l-dC is superior to the well-noted β-d/β-d-dC pair in terms of stability. CD spectra were used to follow global helical changes of DNA structure.

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Thermodynamic Analysis of Duplex Formation of the Heterochiral DNA with l-Deoxyadenosine

Cited by 12 publications

References 43 publications

Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases

Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases

Thermodynamic Features of Structural Motifs Formed by β-L-RNA

Anomeric and Enantiomeric 2’‐Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions

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