Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

DNA conformations and their sequence preferences.

Daniel Svozil1, Jan Kalina, Marek Omelka

  • 1Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, CZ-166 10 Prague, Czech Republic.

Nucleic Acids Research
|May 15, 2008
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The MOlecular-Scale Biophysics Research Infrastructure (MOSBRI) Project and its Outcomes.

European biophysics journal : EBJ·2026
Same author

Tree species influence soil carbon quality but not total storage across horizons: European beech on Dystric Cambisol and Norway spruce on Entic Podzol.

PloS one·2026
Same author

Technical note: a functional data analysis approach to analyze the light-adapted electroretinogram in children and adolescents.

Documenta ophthalmologica. Advances in ophthalmology·2026
Same author

Scaffold-based evaluation metrics for fair comparison of molecular generators.

Journal of cheminformatics·2026
Same author

New targets and procedures for validating the valence geometry of nucleic acid structures.

Nucleic acids research·2026
Same author

DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis.

Nucleic acids research·2026
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

DNA backbone geometry analysis reveals new conformers beyond A, B, and Z forms. Complexed DNA expands conformational space, with sequence preferences identified for recognition.

Area of Science:

  • Structural Biology
  • Biochemistry
  • Molecular Genetics

Background:

  • The DNA phosphodiester backbone's conformation dictates DNA structure and function.
  • Understanding DNA conformational flexibility is crucial for molecular recognition and drug design.

Purpose of the Study:

  • To comprehensively analyze DNA phosphodiester backbone geometry across diverse DNA structures.
  • To identify novel DNA conformers and characterize their occurrence in various DNA states (naked vs. complexed).

Main Methods:

  • Analysis of 7739 dinucleotides from 447 DNA crystal structures.
  • Application of Fourier averaging and clustering techniques to study ten backbone torsion angles.
  • Statistical goodness-of-fit tests to assess sequence preferences.

Related Experiment Videos

Main Results:

  • Identification of known A-, B-, and Z-DNA forms, alongside novel A+B hybrid conformers and syn-base conformers (e.g., in G-quadruplexes).
  • Demonstration of a close relationship between A- and B-form DNA helices through numerous conformers.
  • Observed significant expansion of DNA conformational space in complexed DNA, yet within A- and B-form limits.
  • Assessment of sequence preferences for major A- and B-conformers.

Conclusions:

  • DNA exhibits a richer conformational landscape than previously appreciated, including hybrid and syn-base forms.
  • DNA conformational plasticity is enhanced upon complexation, influencing its interactions.
  • Identified sequence preferences provide insights into DNA recognition mechanisms.