ArticleBiophysical journal1997
Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study.
Article in Biophysical journal, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed, 201 citations in OpenAlex.
- Structure of native four-repeat satellite III sequence with non-canonical base interactions.Nucleic acids research · 2024Article
- Zα Domain of ADAR1 Binds to an A-Form-like Nucleic Acid Duplex with Low Micromolar Affinity.Biochemistry · 2024Article
- Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate.Journal of the American Chemical Society · 2024Article
- Understand the Specific Regio- and Enantioselectivity of Fluostatin Conjugation in the Post-Biosynthesis.Biomolecules · 2020Article
- Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.Scientific reports · 2019Article
- Lone pair-π interactions in biological systems: occurrence, function, and physical origin.European biophysics journal : EBJ · 2017Review
- Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs.Nucleic acids research · 2017Article
- Noncovalent Interactions in the Catechol Dimer.Biomimetics (Basel, Switzerland) · 2017Article
- Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.Genomics data · 2016Article
- 'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.Nucleic acids research · 2016Article
- MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids.Nucleic acids research · 2015Article
- TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.Source code for biology and medicine · 2015Article
- Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs.Nucleic acids research · 2014Article
- Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.Journal of the American Chemical Society · 2013Article
- Guanine base stacking in G-quadruplex nucleic acids.Nucleic acids research · 2013Article
- Promoters of Escherichia coli versus promoter islands: function and structure comparison.PloS one · 2013Article
- In vivo, in vitro, and in silico analysis of methylation of the HIV-1 provirus.Methods (San Diego, Calif.) · 2011Review
- Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli.Journal of bacteriology · 2011Article
- Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?The journal of physical chemistry. B · 2010Article
- Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals.Journal of molecular modeling · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
Abstract
Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied using the ab initio quantum-chemical method with inclusion of electron correlation. The stacking energies in canonical B-DNA base-pair steps vary from -9.5 kcal/mol (GG) to -13.2 kcal/mol (GC). The many-body nonadditivity term, although rather small in absolute value, influences the sequence dependence of stacking energy. The base-stacking energies calculated for CGC and a hypothetical TAT sequence in Z-configuration are similar to those in B-DNA. Comparison with older quantum-chemical studies shows that they do not provide even a qualitatively correct description of base stacking. We also evaluate the base-(deoxy)ribose stacking geometry that occurs in Z-DNA and in nucleotides linked by 2',5'-phosphodiester bonds. Although the molecular orbital analysis does not rule out the charge-transfer n-pi* interaction of the sugar 04' with the aromatic base, the base-sugar contact is stabilized by dispersion energy similar to that of stacked bases. The stabilization amounts to almost 4 kcal/mol and is thus comparable to that afforded by normal base-base stacking. This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.