Nucleic acids, molecules essential for all life, can adopt many alternative structures besides the well-known right-handed double helix, some of which have been reported to exist and function in vivo. One of the most appropriate methods for structural studies of nucleic acids is circular dichroism spectroscopy, utilizing structure-induced chirality due to the asymmetric winding of absorbing nucleobases. Using electronic CD and absorption spectroscopies in combination with melting experiments, we analyzed a conformational equilibrium between DNA double helix and two alternative conformations of nucleic acids, cytosine i-motifs and guanine quadruplexes, as a function of the primary structure of model G/C-rich sequences, containing blocks of G and C runs in particular DNA strands. This paper is a part of special issue dedicated to 70th anniversary of the Biophysical Institute of the Czech Academy of Sciences, where circular dichroism spectroscopy of nucleic acids has been used successfully and impactfully for many years.

• Keywords
• Circular dichroism spectroscopy, Conformation equilibrium, Cytosine i-motif, DNA, Guanine quadruplex,
• Publication type
• Journal Article MeSH

Abasic (AP) lesions are the most frequent type of damages occurring in cellular DNA. Here we describe the conformational effects of AP sites substituted for 2'-deoxyadenosine in the first (ap7), second (ap13) or third (ap19) loop of the quadruplex formed in K(+) by the human telomere DNA 5'-d[AG3(TTAG3)3]. CD spectra and electrophoresis reveal that the presence of AP sites does not hinder the formation of intramolecular quadruplexes. NMR spectra show that the structural heterogeneity is substantially reduced in ap7 and ap19 as compared to that in the wild-type. These two (ap7 and ap19) sequences are shown to adopt the hybrid-1 and hybrid-2 quadruplex topology, respectively, with AP site located in a propeller-like loop. All three studied sequences transform easily into parallel quadruplex in dehydrating ethanol solution. Thus, the AP site in any loop region facilitates the formation of the propeller loop. Substitution of all adenines by AP sites stabilizes the parallel quadruplex even in the absence of ethanol. Whereas guanines are the major determinants of quadruplex stability, the presence or absence of loop adenines substantially influences quadruplex folding. The naturally occurring adenine-lacking sites in the human telomere DNA can change the quadruplex topology in vivo with potentially vital biological consequences.

• MeSH
• Adenine chemistry   MeSH
• Potassium chemistry   MeSH
• G-Quadruplexes * MeSH
• Guanine chemistry   MeSH
• Humans MeSH
• Models, Molecular MeSH
• Nuclear Magnetic Resonance, Biomolecular MeSH
• DNA Damage * MeSH
• Telomere chemistry   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Adenine MeSH
• Potassium MeSH
• Guanine MeSH

Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex-forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures-some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3'UTR (but were also present in 5'UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements.

• MeSH
• DNA, Plant chemistry   MeSH
• G-Quadruplexes * MeSH
• Genome, Plant MeSH
• Terminal Repeat Sequences * MeSH
• Retroelements * MeSH
• Sequence Analysis, DNA MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA, Plant MeSH
• Retroelements * MeSH

Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.

• MeSH
• DNA, A-Form chemistry   MeSH
• Circular Dichroism * MeSH
• Nucleic Acid Denaturation MeSH
• DNA chemistry   MeSH
• G-Quadruplexes MeSH
• Nucleic Acid Conformation MeSH
• DNA, Z-Form chemistry   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• DNA, A-Form MeSH
• DNA MeSH
• triplex DNA MeSH Browser
• DNA, Z-Form MeSH