scholarly journals Hachimoji DNA and RNA: A genetic system with eight building blocks

Science ◽  
2019 ◽  
Vol 363 (6429) ◽  
pp. 884-887 ◽  
Author(s):  
Shuichi Hoshika ◽  
Nicole A. Leal ◽  
Myong-Jung Kim ◽  
Myong-Sang Kim ◽  
Nilesh B. Karalkar ◽  
...  
Keyword(s):  
Double Helix ◽  
Building Blocks ◽  
Genetic System ◽  
Molecular Structures ◽  
Darwinian Evolution ◽  
Structural Requirements ◽  
Dna And Rna ◽  
The Stability ◽  
Dna Double Helix ◽  
Orthogonal Pairs

We report DNA- and RNA-like systems built from eight nucleotide “letters” (hence the name “hachimoji”) that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.

scholarly journals Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

2014 ◽  
Vol 10 ◽  
pp. 1589-1595 ◽  
Author(s):  
Christian B Winiger ◽  
Simon M Langenegger ◽  
Oleg Khorev ◽  
Robert Häner
Keyword(s):  
Double Helix ◽  
Building Blocks ◽  
Supramolecular Interactions ◽  
Stacking Interactions ◽  
Average Value ◽  
Π Stacking ◽  
Dna Strands ◽  
Polycyclic Aromatic ◽  
The Stability ◽  
Dna Double Helix

Aromatic π–π stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA–polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene–PDI interactions that were found to directly influence duplex stability. As the pyrene–PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene–PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic π–π stacking interactions.

scholarly journals MUTABLE R-NAVAJO ALLELES OF CYCLIC ORIGIN IN MAIZE

Genetics ◽  
1973 ◽  
Vol 73 (2) ◽  
pp. 273-296
Author(s):  
R Alexander Brink ◽  
Elizabeth Williams
Keyword(s):  
Nucleotide Sequence ◽  
Gene Action ◽  
Double Helix ◽  
Donor Site ◽  
Chromosome Breakage ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Unstable Compound ◽  
The Stability ◽  
Dna Double Helix

ABSTRACT The generation in cyclic fashion of 26 mutable R-Navajo (mRnj) alleles in maize involved transposition of a non-specific repressor of gene action, Modulator (Mp), first away from, and then back to, the R locus represented by the R-Navajo (Rnj) all ele on chromosome 10. The mPnj alleles reconstituted in this way vaned widely, and continuously, in mutability to Rnj-that is, in transposition of Mp away from the R locus, thus derepressing the Rnj gene. They were alike, or nearly so, however, in activating Ds chromosome breakage and in increasing the stability of variegated pericarp, another unstable compound allele comprising Mp conjoined with Prr on chromosomal 1. These latter two phenomena are based primarily on loci elsewhere in the genome. It is postulated that the 26 reconstituted mRnj alleles carry a common Mp which, however, is intercalated at a different site within each allele. Nucleotide sequence in the regions adjacent to Mp is assumed to determine the frequency with which a form of micro-nondisjunction occurs whereby Mp is released from a donor site. Transposition to a new site is interpreted in terms of a chromosome model that gives effect to nicking, or single strand breaks, occurring throughout the genome as a prerequisite to unwinding, strand separation, and replication, of the DNA double helix.

scholarly journals Untersuchungen über die Bindung pflanzlicher Wuchsstoffe an verschiedene Komponenten des Chromatins in vitro. I. Bindung an DNS / Investigations Upon the Binding of Plant Growth Substances to Several Components of the Chromatin in vitro. I. Binding to DNA

1971 ◽  
Vol 26 (6) ◽  
pp. 607-612 ◽  
Author(s):  
Günter Fellenberg
Keyword(s):  
Hydrogen Bonds ◽  
Absorption Maximum ◽  
Double Helix ◽  
Specific Effect ◽  
Growth Substance ◽  
Growth Substances ◽  
Plant Growth Substances ◽  
The Stability ◽  
Dna Double Helix

At pH 9,5 the DNA absorption maximum at 190 nm was shifted to 212 nm. This absorption maximum showed a bathochrome effect in the presence of IAA, GA and KI. The amplitude of this maximum was reduced at the same time. By addition of urea (0.1 —2.0 moles/l) the bathochrome effect, induced by the growth substances, was completely reversed, whereas application of NaCl (0.1 — 2.0 moles/l) did not affect the bathochrome movement of this DNA maximum. At pH 6.0 in the presence of 0.9% NaCl this DNA maximum did not show any visible bathochrome movement in the presence of the growth substances investigated. The DNA maximum at 260 nm did not show any alteration in the presence of growth substances.The thermal denaturation of DNA-complexes with IAA and GA showed, that with increasing concentration of these growth substances, the Tm-value of the DNA was reduced. On the other hand, KI increased the Tm-point of DNA. By biphasic melting at 260 nm and 280 nm no specific effect of the investigated growth substances on the stability of the A — T or G—C pairs was detected.Tryptophan and β-NAA closely related in structure to the auxins IAA and α-NAA did not reduce the Tm-value of DNA.At pH < 7 IAA, GA and KI did not show any detectable influence on the Tm-value of DNA.The data presented show that at a pH > 7 IAA, GA and KI are obviously bound to DNA by hydrogen bonds. There is evidence that these bonds are very unstable. Nevertheless, IAA and GA can loosen part of the hydrogen bonds of DNA double helix while KI cannot. Possible consequences of these growth substance effects on DNA are discussed.

Viscometric Studies on the Stability of DNA-Proflavine Complex

1972 ◽  
Vol 27 (11) ◽  
pp. 1385-1387 ◽  
Author(s):  
G. C. Das ◽  
N. N. Das Gupta
Keyword(s):  
Double Helix ◽  
Thermal Stabilization ◽  
Binding Mode ◽  
Stable Configuration ◽  
P Value ◽  
Binding Modes ◽  
Specific Viscosity ◽  
Complex Variation ◽  
The Stability ◽  
Dna Double Helix

Viscometric technique has been used to estimate the relative contributions of strong and weak binding modes towards thermal stabilization of the Proflavine-DNA complex. Variation of the ratio of the specific viscosity of the dye-bound DNA to that of the DNA solution (η′sp/η sp) with different dye to DNA-phosphate ratios (D/P) shows that the saturation is attained at D/P value of about 0.2. This effect is more pronounced at lower ionic strengths. Heat-induced helix-coil transition curves at different D/P values at a fixed ionic strength of the buffer reveal a gradual shift towards higher temperature with the increase of D/P and levelling off at D/P of about 0.22. It is suggested that only the strong binding mode causes thermal stabilization of the DNA double helix and the double helix having all the possible intercalating sites saturated by the dye molecules attains the most stable configuration.

Synthesis and structure of fluoroindole nucleosides

2007 ◽  
Vol 85 (4) ◽  
pp. 283-292 ◽  
Author(s):  
Jelena Božilović ◽  
Jan W Bats ◽  
Joachim W Engels
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Driving Forces ◽  
Rna Stability ◽  
Building Blocks ◽  
Biologically Active ◽  
Dna And Rna ◽  
The Stability ◽  
Indole Synthesis

Chemically modified bases are frequently used to stabilize nucleic acids, to study the driving forces for nucleic acid structure formation, and to tune DNA and RNA hybridization conditions. Nucleoside analogues are chemical means to investigate hydrogen bonds, base stacking, and solvation as the three predominant forces that are responsible for the stability of nucleic acids. To obtain deeper insight into the contributions of these interactions to RNA stability, we decided to synthesize some novel nucleic acid analogues where the nucleobases are replaced by fluoroindoles. Fluorinated indoles can be compared with fluorinated benzimidazoles to determine the role of nitrogen in five-membered ring systems. The synthesis of fluoroindole ribonucleosides as well as the X-ray crystal structures of all synthesized fluoroindole ribonucleosides are reported here. These compounds could also be building blocks for a variety of biologically active RNA analogues.Key words: indoles, nucleosides, crystal structure, glycosilation, indole-synthesis.

scholarly journals Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA

2021 ◽  
Author(s):  
Honglue Shi ◽  
Issac Kimsey ◽  
Hsuan-Fu Liu ◽  
Uyen Pham ◽  
Maria Schumacher ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Genetic Information ◽  
Double Helix ◽  
Building Blocks ◽  
Base Pairs ◽  
Dna Complexes ◽  
Damage Repair ◽  
Functional Complexity ◽  
Dna Double Helix ◽  
Broad Role

Watson-Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative 'Hoogsteen' bps, expanding the functional complexity of DNA. We developed 'Hoog-finder', which uses structural fingerprints to rapidly screen Hoogsteen bps, which may have been mismodeled as Watson-Crick in crystal structures of protein-DNA complexes. We uncovered seventeen Hoogsteen bps, seven of which were in complex with six proteins never before shown to bind Hoogsteen bps. The Hoogsteen bps occur near mismatches, nicks, and lesions and some appear to participate in recognition and damage repair. Our results suggest a potentially broad role for Hoogsteen bps in stressed regions of the genome and call for a community-wide effort to identify these bps in current and future crystal structures of DNA and its complexes.

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