Novel DNA Catalysts Based on G‐Quadruplex Recognition

Tang, Zhuo; Gonçalves, Diana P. N.; Wieland, Markus; Marx, Andreas; Hartig, Jörg S.

doi:10.1002/cbic.200800024

Cited by 53 publications

(43 citation statements)

References 113 publications

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“…Reports of such nanomachines date back to 1999 when Seeman and coworkers built a DX tileÀbased device containing a double-stranded d(CG) 10 linker [41] that was converted from B-DNA to left-handed Z-DNA at high ionic conditions. Since then various other DNA nanomachines have been reported, including DNA tweezers driven by hybridization of complementary strands, [42,43] catalytic DNA, [43,44] G-rich quadruplexes, [45,46] and i-motifs. [47,48] In recent years there has been a great deal of interest in DNA computing, with reports of the construction of a series of DNA logic gates and higher-order DNA circuits [49][50][51][52][53] that produce output signals based on various inputs (usually DNA strands).…”

Section: Functionalized Dna Nanostructures For Disease Diagnosismentioning

confidence: 99%

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Functionalized DNA Nanostructures for Nanomedicine

Liu

Yan

2013

Israel Journal of Chemistry

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DNA nanotechnology utilizes synthetic DNA strands as the building material to construct nanoscale devices, and the field has developed rapidly over the past decade. Recently, the use of DNA nanostructures for various applications, particularly biomedical ones, has drawn great interest. This review focuses on the most recent research directed at utilizing functionalized DNA devices for nanomedical applications and presents representative research progress in disease diagnosis, treatment and prevention. In addition, the safety and future clinical applications of DNA nanostructures are discussed.

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Section: Functionalized Dna Nanostructures For Disease Diagnosismentioning

confidence: 99%

“…a) Nanomechanical device based on the B-Z transition of DNA. [41] b) Illustration of a DNA nanotweezer driven by various environmental stimuli (hybridization of complementary DNA, [42,43] catalytic DNA, [44] changes in pH, [47,48] and ion concentration [45,46] ). c) Representative DNA logic gate.…”

Section: Functionalized Dna Nanostructures For Disease Diagnosismentioning

confidence: 99%

Functionalized DNA Nanostructures for Nanomedicine

Liu

Yan

2013

Israel Journal of Chemistry

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“…Several of the modified TBAs were capable of catalysing the reaction, some with yields in excess of 80% within 24 hrs, thus the thrombin-binding aptamer, which bound the porphyrin, was capable of assisting in the catalysis of the reaction. 391 The methodology for selection of aptamers was first described using RNA, and much of the early work was carried out with RNA. Since it was found that DNA can also be used for developing aptamers, and DNA is more stable, the number of RNA aptamers has reduced.…”

Section: Aptamers and (Deoxy)ribozymesmentioning

confidence: 99%

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

Loakes

2010

Organophosphorus Chemistry

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“…This approach is not limited to common metals in biology, as o b se r v e d in a n Ir + -diene-dependent allylic substitution catalyst [18]. Cofactors such as bipyridines [17], polyaza crown ethers [50], dienes [18], and metalloporphyrins [51] have been introduced by intercalation or clever use of the G-quadruplex motif of DNA. Chelation of metal ions in proteins is the essence is much of biological catalysis.…”

Section: Metal Ions As Cofactors: Enhanced Reactivity Of Chiral Dna Smentioning

confidence: 99%

Thermodynamics of Nucleic Acid Structural Modifications for Biotechnology Applications

Franzen¹

2011

Biotechnology of Biopolymers

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IntroductionThe repertoire of chemistry available to native nucleotides in DNA and RNA is limited to the purine and pyrimidine functional groups, along with the special role of the 2'-hydroxyl of RNA. The nucleobases have exocyclic amino groups and imines, neither of which is highly reactive or a good candidate for catalytic function. One might argue that the limited range of chemical reactivity is an evolutionary advantage in molecules whose functions are primarily to store (DNA) and process (RNA) genetic information. The most important attribute of both DNA and RNA is the molecular recognition through base pairing. The hydrogen bond pattern combined with the conformation of the ribose sugar gives rise to the specific B-form double helix in DNA and A-form helix with a range of additional standard folds in RNA, loops, bulges and pseudoknots. These structures are well known for their ability to interact with proteins to provide a scaffold for transcription (DNA → RNA) to create messenger RNA (mRNA), and processing of mRNA by enzymes that have active components composed of RNA molecules. The chemical action of RNA on other RNAs by means of the 2'-hydroxyl is an exception to the lack or reactivity of DNA and RNA. Selfsplicing by action of the 2'-hydroxyl as a nucleophile was the process that broke the dogma that RNA is always a passive molecule that simply transmits information [1]. Indeed, RNA i s v e r y a c t i v e i n p r o c e s s i n g o t h e r R N A s u s i n g t h e 2 ' -h y d r o x y l a s a n u c l e o p h i l e f o r hydrolysis of the phosphodiester bond leading to cleavage or to rearrangements of structure such as RNA splicing. Outside of this reactivity, the components of the purine and pyrimidine rings are largely inert. Aromatic amines are poor nucleophiles, and imines are even less reactive. The purine and pyrimidine rings are not particularly electrophilic because of the nitrogen heteroatoms and carbonyls. Using in vitro selection (also known as SELEX) [2][3][4], and appropriate modification, RNA and DNA have been developed for numerous applications that transcend their biological functions. In this chapter we will consider the modifications of the nucleobase as a means to expand upon the native function. The extensive literature on modifications of the phosphodiester backbone and the ribose sugar will not be considered in this chapter due to space limitations. Base modifications may consist of expansions of the purine/pyrimidine ring, appended functional group or chemical modification to increase the stability of the backbone with respect to hydrolysis. Expanded DNA or xDNA has been developed as mimics of native DNA with potential biotechnology applications [5,6]. In these molecules, the purine and pyrimidine rings are fused to phenyl or naphthyl rings to give rise to

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Novel DNA Catalysts Based on G‐Quadruplex Recognition

Cited by 53 publications

References 113 publications

Functionalized DNA Nanostructures for Nanomedicine

Functionalized DNA Nanostructures for Nanomedicine

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

Thermodynamics of Nucleic Acid Structural Modifications for Biotechnology Applications

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