The co-association of nucleosides and the equilibrium copolymerization of nucleotides. Base stacking interactions and the thermodynamics of phosphodiester bond formation

1976 ◽  
Vol 80 (22) ◽  
pp. 2462-2467 ◽  
Author(s):  
Leonard Peller
Keyword(s):  
Bond Formation ◽  
Stacking Interactions ◽  
Base Stacking ◽  
Phosphodiester Bond

scholarly journals Bending and Base-Stacking Interactions in Double-Stranded DNA

1999 ◽  
Vol 82 (22) ◽  
pp. 4560-4563 ◽  
Author(s):  
Zhou Haijun ◽  
Zhang Yang ◽  
Ou-Yang Zhong-can
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna

scholarly journals Selective recognition of human telomeric G-quadruplex with designed peptide via hydrogen bonding followed by base stacking interactions

RSC Advances ◽  
2019 ◽  
Vol 9 (69) ◽  
pp. 40255-40262 ◽  
Author(s):  
Shikhar Tyagi ◽  
Sarika Saxena ◽  
Nikita Kundu ◽  
Taniya Sharma ◽  
Amlan Chakraborty ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Synthetic Peptide ◽  
High Selectivity ◽  
Selective Recognition ◽  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna ◽  
G Quadruplex ◽  
Guanine Base

A new synthetic peptide is presented. A Glu residue binds through H-bonding to a guanine-base and a Trp residue intercalates with K+ resulting in stabilization of a human telomeric G-quadruplex with high selectivity over a complementary c-rich strand and double-stranded DNA.

scholarly journals Structural intermediates of a DNA–ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation

2019 ◽  
Vol 47 (14) ◽  
pp. 7147-7162 ◽  
Author(s):  
Adele Williamson ◽  
Hanna-Kirsti S Leiros
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
Bond Formation ◽  
Strand Break ◽  
Nucleophilic Attack ◽  
Dna Ligase ◽  
Phosphodiester Bond ◽  
Dna Ligases ◽  
Catalytic Metal ◽  
Ternary Structure

Abstract DNA ligases join adjacent 5′ phosphate (5′P) and 3′ hydroxyl (3′OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase–DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3′OH terminus for nucleophilic attack on the 5′P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.

scholarly journals In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole–activated substrates

2020 ◽  
Vol 117 (11) ◽  
pp. 5741-5748 ◽  
Author(s):  
Travis Walton ◽  
Saurja DasGupta ◽  
Daniel Duzdevich ◽  
Seung Soo Oh ◽  
Jack W. Szostak
Keyword(s):  
Origin Of Life ◽  
In Vitro Selection ◽  
Random Sequence ◽  
Bond Formation ◽  
Rna Sequences ◽  
Phosphodiester Bond ◽  
Complex Protein ◽  
The Origin Of Life ◽  
Group 2

The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5′-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide–activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3′-5′ phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.

BENDING AND BASE-STACKING INTERACTIONS IN DOUBLE-STRANDED DNA

APPC 2000 ◽  
2001 ◽  
Author(s):  
HAIJUN ZHOU ◽  
YANG ZHANG ◽  
ZHONG-CAN OU-YANG
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna

scholarly journals Distributed chaos in DNA

2018 ◽  
Author(s):  
A. Bershadskii
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequence ◽  
Kam Theory ◽  
Translational Symmetry ◽  
Stacking Interactions ◽  
Dna Dynamics ◽  
Base Stacking ◽  
Genetic Sequencing ◽  
Model Plant ◽  
Human Genes

It is shown that distributed chaos, generated by Hamiltonian DNA dynamics with spontaneously broken time translational symmetry, imprints itself on the DNA sequence of Arabidopsis thaliana (a model plant for genetic sequencing and mapping) and of the NRXN1 and BRCA2 human genes (as an example). The base-stacking interactions in the DNA duplex, degenerate codon groups and a relation to the KAM theory have been discussed in this context.

scholarly journals A comprehensive survey on the nature of ring:ring nucleobase stacking interactions in RNA: occurrence, structural variability and classification of the associated contacts

2020 ◽  
Author(s):  
Ayush Jhunjhunwala ◽  
Zakir Ali ◽  
Sohini Bhattacharya ◽  
Antarip Halder ◽  
Abhijit Mitra ◽  
...  
Keyword(s):  
Classification System ◽  
Classification Scheme ◽  
Relative Orientation ◽  
Stacking Interactions ◽  
Automated Identification ◽  
Base Stacking ◽  
Base Pairs ◽  
Glycosidic Bonds ◽  
Comprehensive Survey

ABSTRACTThe astonishing diversity in folding patterns of RNA 3D structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. Although the classification scheme proposed by Leontis and Westhof (RNA (2001), 7, 499) has been widely accepted for the annotation of RNA base pairs, the absence of an unambiguous classification system for base stacks appears to be a roadblock for exploring the stacking diversity in RNA. Here we provide an unambiguous and structurally-intuitive scheme for a geometry cum topology based classification of base stacking, where a stack is essentially classified in terms of the topology of the interacting nucleobase faces and the geometry described by the relative orientation of the glycosidic bonds. For heterodimeric stacks, this generates eight basic stacking geometric families, whereas for homodimeric stacks, this generates six of those. Further annotation in terms of the identity of the bases and the region of involvement of purines (5-membered, 6-membered or both rings), leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we also present an algorithm for automated identification of stacks in RNA crystal structures. Overall, the work described here is expected to greatly facilitate structure-based RNA research.

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