A Nanothermometer Based on the Different π Stackings of B‐ and Z‐DNA

Tashiro, Ryu; Sugiyama, Hiroshi

doi:10.1002/anie.200352752

Cited by 78 publications

(40 citation statements)

References 19 publications

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“…A 2AP undergoing base extrusion could be utilized as a highly sensitive biosensor responding to changing environments such as temperature (16,17). In addition, understanding of junction structures occurring in double helical nucleic acids would greatly assist our understanding of the roles of these versatile junctions that reverse handedness of double helices.…”

Section: Discussionmentioning

confidence: 99%

Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA

Kim¹,

Reddy²,

Kim³

et al. 2009

Nucleic Acids Research

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Base extrusion is a major structural feature at the junction between B- and Z-DNA (the B–Z junction) where a base pair is broken, and the two bases are extruded from the double helix. Despite the demonstration of base extrusion at the B–Z junction, it is not clear whether a similar base extrusion occurs at other types of junctions involving the left-handed Z conformation. Here, we investigate structural changes of bases at three Z-form junctions: DNA B–Z and Z–Z and RNA A–Z junctions. By monitoring fluorescently labeled duplex nucleic acids using 2-aminopurines at various positions relative to the junction point, we show that base extrusion occurs not only at the DNA B–Z junction, but also at the RNA A–Z and DNA Z–Z junctions. Our data suggest that base extrusion is a general feature of Z-form nucleic-acid junctions.

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Section: Discussionmentioning

confidence: 99%

Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA

Kim¹,

Reddy²,

Kim³

et al. 2009

Nucleic Acids Research

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“…Second, we cannot exclude the possibility that the 2AP is incorporated into a Z-DNA helix rather than adopting a flipped out conformation. Prior studies have shown that 2AP undergoes ~10X enhancement in fluorescence intensity upon transitioning from B-DNA to Z-DNA 39 . This can be attributed to a loss of stacking interactions since in Z-DNA, the 2AP only stacks with its 3′ neighboring base (Figure 1).…”

Section: Resultsmentioning

confidence: 99%

Incorporation of CC Steps into Z-DNA: Interplay between B–Z Junction and Z-DNA Helical Formation

2012

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The left-handed DNA structure, Z-DNA, is believed to play important roles in gene expression and regulation. Z-DNA forms sequence-specifically with a preference for sequences rich in pyrimidine/purine dinucleotide steps. In vivo, Z-DNA is generated in the presence of negative supercoiling or upon binding proteins that absorb the high energetic cost of the B-to-Z transition including the creation of distorted junctions between B-DNA and Z-DNA. To date, the sequence-preferences for the B-to-Z transition have primarily been studied in the context of sequence repeats lacking B/Z junctions. Here, we develop a method to characterize sequence-specific preferences for Z-DNA formation and B/Z junction localization within heterogeneous DNA duplexes that is based on combining 2-aminopurine fluorescence measurements with a new quantitative application of CD spectroscopy for determining the fraction of B- versus Z-DNA. Using this approach, we show that at least three consecutive CC dinucleotide steps, traditionally thought to disfavor Z-DNA, can be incorporated within heterogeneous Z-DNA containing B/Z junctions upon binding to the Zα domain of the RNA adenosine deaminase (ADAR1) protein. Our results indicate that the incorporation of CC steps into Z-DNA is driven by favorable sequence-specific Z/Z and B/Z stacking interactions as well as by sequence-specific energetics that localize the distorted B/Z junction at flexible sites. Together, our results expose higher order complexities in the Z-DNA code within heterogeneous sequences and suggest that Z-DNA can in principle propagate into a wider range of genomic sequence elements than previously thought.

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“…However, the fluorescence of this decamer increased proportionally when the ratio of Z-conformation was increased by increasing the NaCl concentration. 78 These results indicated that the restricted charge-transfer between different four-base -stacks of Z-DNA compared with B-DNA could be monitored by the fluorescence of Ap. We also designed a molecular thermometer based on the change in electronic properties when converting from B-to Z-DNA.…”

Section: Monitoring Conformational Change Of B-z Formmentioning

confidence: 87%

Chemical Biology that Controls DNA Structure and Function: Lessons in Organic Chemistry from Nature

Sugiyama¹

2007

Bulletin of the Chemical Society of Japan

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Fifty years after the discovery of the double-helical structure of DNA, the complete sequence of the human genome has been determined. All genetic information, which is necessary for life, is written in 30 billion base pairs of DNA. Many diseases, including cancer, and hereditary and viral diseases, can now be understood at the DNA sequence level. Local DNA conformations are also thought to play an important role in biological processes, such as gene expression. Therefore, DNA sequences and local DNA conformations are the targets of novel drugs that would precisely switch certain genes on or off. Modified bases that perform various functions can also be incorporated into defined DNA sequences. DNA can now be synthesized by the phosphoramidite method and amplified by PCR, and by using organisms such as Escherichia coli, DNA becomes a promising unit for nanotechnology applications. In this review, I focus on our efforts in understanding the DNA reactivity, structure, and function of DNA. The prospective uses of the chemical biology of DNA will also be discussed.Chemistry has greatly contributed to the understanding of cellular processes by allowing the identification of metabolic pathways, enzymatic processes, and signal transduction mechanisms. Understanding of the chemistry of nucleic acids has played a key role in the progressive development of molecular biology and life science through the development of many epoch-making techniques, such as the DNA sequencing, the synthesis of oligonucleotides, and PCR amplification. During my Ph.D. course, I started research on photochemistry between DNA and proteins as a model of photoinduced DNA-protein crosslinking for examining the ternary structure of the nucleosome and understanding the mechanisms of photodamage of DNA. We found that the "-amino group of the lysine residues of histone crosslinked with thymine residues in DNA.1 Interestingly, the crosslink site was cleaved upon heating to regenerate the thymine ring on the "-amino group of the lysine residues in the protein by Michael addition (Figure 1). At that time, not so many researchers were interested in chemical modification in a nucleosome.Because we applied this photoreaction for T specific cleavage of DNA, 1d I was attracted to the molecular mechanisms of DNA modification at an atomic level. I had the chance to study the mechanism of action of the antitumor antibiotic bleomycin at Sidney Hecht's group at the University of Virginia from 1984 to 1986. We investigated how these glycopeptides recognize specific DNA sequences and efficiently oxidize C4 0 deoxyribose to induce DNA strand cleavage using synthetic oligonucleotides with defined sequences. 2 We identified the formation of C4 0 hydroxy abasic sites in addition to the known oxidative direct-strand scission via a Criegee type rearrangement of the C4 0 hydroperoxy intermediate. 3 We found that the C4 0 hydroxy abasic site generated by Fe-bleomycin underwent aldol condensation and subsequent elimination and rearrangement to produce cyclic hydroxy pentenon...

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A Nanothermometer Based on the Different π Stackings of B‐ and Z‐DNA

Cited by 78 publications

References 19 publications

Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA

Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA

Incorporation of CC Steps into Z-DNA: Interplay between B–Z Junction and Z-DNA Helical Formation

Chemical Biology that Controls DNA Structure and Function: Lessons in Organic Chemistry from Nature

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