Circular dichroism (CD) spectroscopy is a fast and simple technique providing important information about the conformation of macromolecules, includnig nucleic acids, proteins, sugars, lipids, and their interactions between each other. This electronic absorption spectroscopy method is extremely sensitive to any change in molecular structure containing asymmetric molecules ( Reid Bishop & Chaires, 2002). Physically, CD assesses the absorption of light due to excitation of electronic transitions by the near and parts of the far-UV light (300–200 nm for near and 200–170 nm for the far UV in aqueous solutions). CD is sensitive to the differential absorption of circularly left- and right-polarized light due to electronic transitions ( Hu et al. 2002) such as the n-π or π-π∗ transitions of chiral molecules including nucleic acids. Asymmetric sugars in nucleic acids, including deoxyriboses and riboses, induce a circular dichroism absorption on the symmetrical bases. Moreover, the spatial arrangement of RNA and DNA molecules in helices and loops forming asymmetric molecules causes a strong CD absorption. For decades, CD has been used to follow conformational and structural changes of nucleic acid macromolecules in solution at different pHs, ionic strengths, or temperatures. In addition, CD can detect their interactions with achiral and chiral molecules including proteins.

NACDDB hosts a series of experiments originating from the synchrotron SOLEIL, as well as data adopted from the literature. The experimental data include the spectra of DNA, RNA, DNA/RNA hybrids, and other nucleic acid molecules. Importantly, all datasets are carefully analyzed and validated by CD experts. We also present 3D structural models for the nucleic acid molecules analyzed (generated without the use of CD data) to illustrate the structural complexity of the molecules analyzed.

For improvements or suggestions, please use our contact form. Please use the contact form also to notify us if you want to provide us with new data. We will get back to you as soon as possible discussing about the data and the format. Proposed spectra must have been pubished !

Currently, we are populating the NACDDB database with CD datasets and our main task is to validate the CD spectra by experts. Our next step is to present a set of reference spectra for specific structural features of nucleic acids. For the next version, we plan to implement prediction tools based on machine learning using CD data as an important contribution to RNA structure determination.

The NACDDB website is free, open to all users and there is no login required. The data is freely accessible for research and academic purposes. Industry users interested in commercial use of NACDDB data are encouraged to contact us.

NACDDB hosts nucleotide sequences with modified residues. Each modified nucleotide is represented with the standard notation used in the MODOMICS database. Furthermore, each of the modified residue contains a link to the relative page of the MODOMICS database.

NACDDB presents data for many different types of nucleic acid structures. The basic classification includes the following classes:

1. ss : single stranded (non-base paired single-stranded nucleic acid

2. ds : doubled stranded (duplex involving canonical (A•T, G•C, A•U) or Hoogsteen base pairs; specific duplexes can be antiparallel or parallel)

3. ts : triple stranded (structure involving canonical duplex and a 3rd Pu or Py strand paired using Hoogsteen hydrogen bonds)

4. qs : quadruple stranded (structure involving base pairing among 4 strands of nucleic acid; in a G-quadruplex, guanines form a ring stabilized by Hoogsteen hydrogen bonds and 3 or more rings stack into a 4-stranded structure comprised of parallel or antiparallel strands)

5. g : genomic (mixed sequence sample comprised of an entire genome

6. i-motif : i-motif (tetrameric structure from two intercalated (C•C+)n duplexes

Moiety Subtypes, useful for searching the database, include :

Many experiments are related to multimers. Different chains are marked with 5' and 3' so that beginnings and endings of each sequence can be easily distinguished.