Recognition of nucleic acid double helices by homopyrimidine 2',5'-linked RNA

Damha, Masad J.; Noronha, Anne M.

doi:10.1093/nar/26.22.5152

Cited by 12 publications

(9 citation statements)

References 48 publications

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“…It is now well established that nucleic acids, even with 2′,5′ linkages, associate to form Watson and Crick paired duplexes [2–5,10,11,32–37]. They also selectively associate with DNA and RNA with a varying degree of stability.…”

Section: Discussionsupporting

confidence: 74%

Solution structure of 2′,5′ d(G₄C₄)

Premraj

Raja

Bhavesh

et al. 2004

European Journal of Biochemistry

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The NMR structure of 2¢,5¢ d(GGGGCCCC) was determined to gain insights into the structural differences between 2¢,5¢-and 3¢,5¢-linked DNA duplexes that may be relevant in elucidating nature's choice of sugar-phosphate links to encode genetic information. The oligomer assumes a duplex with extended nucleotide repeats formed out of mostly N-type sugar puckers. With the exception of the 5¢-terminal guanine that assumes the syn glycosyl conformation, all other bases prefer the anti glycosyl conformation. Base pairs in the duplex exhibit slide ()1.96 Å ) and intermediate values for X-displacement ()3.23 Å ), as in ADNA, while their inclination to the helical axis is not prominent. Major and minor grooves display features intermediate to A and BDNA. The duplex structure of iso d(GGGGCCCC) may therefore be best characterized as a hybrid of A and BDNA. Importantly, the results confirm that even 3¢ deoxy 2¢,5¢ DNA supports duplex formation only in the presence of distinct slide ( ‡ )1.6 Å ) and X-displacement ( ‡ )2.5 Å ) for base pairs, and hence does not favor an ideal BDNA topology characterized by their near-zero values. Such restrictions on base pair movements in 2¢,5¢ DNA, which are clearly absent in 3¢,5¢ DNA, are expected to impose constraints on its ability for deformability of the kind observed in DNA during its compaction and interaction with proteins. It is therefore conceivable that selection pressure relating to the optimization of topological features might have been a factor in the rejection of 2¢,5¢ links in preference to 3¢,5¢ links.Keywords: structure of 2¢,5¢ DNA; evolution of 3¢,5¢ vs. 2¢,5¢ links in nucleic acids; AB hybrid structure; restrained base pair movements; topological restrictions in 2¢,5¢ DNA.Nature's selection of 3¢,5¢ linkages (instead of 2¢,5¢ linkages) in nucleic acids, to encode genetic information, is intriguing. The fact that 2¢,5¢ links are formed in abundance and serve as a template in nonenzymatic reactions suggest that they might have been the ancestors of the biotic 3¢,5¢ links, which could have evolved from a pool of 3¢,5¢ and 2¢,5¢ links [1]. Nucleic acids with 2¢,5¢ links satisfy one of the critical features required for the fidelity of replication, namely that they associate to form Watson and Crick base-paired duplex structures [2][3][4][5], although with weaker affinity than 3¢,5¢-linked DNA strands. However, detailed knowledge about stereochemistry, polymorphism and topological properties of 2¢,5¢ DNA duplexes, which may provide insights into the factors that determine nature's choice of sugar-phosphate links from a stereochemical perspective, is sparse [6][7][8][9]. In fact, there are only two reports of NMR structure determination -one on a 2¢,5¢ DNA fragment [10] and one on a 2¢,5¢ RNA fragment [11] -both of which suggest an A-type duplex structure with some stereochemical details that differ from genomic DNA and RNA duplexes. In this context, it is relevant to recognize the results from recent modeling studies on 2¢,5¢ nucleic acids, which suggest that 2¢,5¢ DNA can...

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Section: Discussionsupporting

confidence: 74%

Solution structure of 2′,5′ d(G₄C₄)

Premraj

Raja

Bhavesh

et al. 2004

European Journal of Biochemistry

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“…There are eight possible combinations of DNA and RNA strands in a triplex. Roberts and Crothers (19) (20,21) confirmed and extended the Roberts and Crothers (19) results with the same hairpin duplex sequences. Other workers used relatively long Watson-Crick duplexes to make partial triplexes with short Hoogsteen-paired third strands (22)(23)(24).…”

Section: Introductionsupporting

confidence: 53%

“…CD spectra have been an important means of characterizing nucleic acid structures, including triplexes, as a function of solution conditions or nucleotide modifications (18,19,21,27,32,38,42,(50)(51)(52)(53). CD spectra are generally very sensitive to slight differences in nucleic acid structures.…”

Section: Spectra Of Triplexes Are Dominated By Hoogsteen Pairingmentioning

confidence: 99%

Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes

Hashem

Wen

et al. 1999

Nucleic Acids Research

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The pyr*pur.pyr type of nucleic acid triplex has a purine strand that is Hoogsteen-paired with a parallel pyrimidine strand (pyr*pur pair) and that is Watson-Crick-paired with an antiparallel pyrimidine strand (pur.pyr pair). In most cases, the Watson-Crick pair is more stable than the Hoogsteen pair, although stable formation of DNA Hoogsteen-paired duplexes has been reported. Using oligomer triplexes of repeating d(AG)12 and d(CT)12 or r(CU)12 sequences that were 24 nt long, we found that hybrid RNA*DNA as well as DNA*DNA Hoogsteen-paired strands of triplexes can be more stable than the Watson-Crick-paired strands at low pH. The structures and relative stabilities of these duplexes and triplexes were evaluated by circular dichroism (CD) spectroscopy and UV absorption melting studies of triplexes as a function of pH. The CD contributions of Hoogsteen-paired RNA*DNA and DNA*DNA duplexes were found to dominate the CD spectra of the corresponding pyr*pur.pyr triplexes.

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“…[4 -6] Stable tri plex formation between the tri plex-forming oligonucleotide (TFO) and the target double-stranded DNA is fundamental to the antigene strategy to regulate gene expression in a living cell. [7] Here we would like to describe that appropriate incorporation of the 2',5'-linkages into TFOs significantly enhances tri plex stability under physiological conditions. [7] Here we would like to describe that appropriate incorporation of the 2',5'-linkages into TFOs significantly enhances tri plex stability under physiological conditions.…”

Section: Introductionmentioning

confidence: 99%