New Reagents for the Introduction of Reactive Functional Groups into Chemically Synthesized DNA Probes

Skrzypczynski, Z.; Wayland, Sarah

doi:10.1021/bc025657j

Cited by 15 publications

(22 citation statements)

References 93 publications

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“…Issues of this enzymatic insertion include the limited types of modified nucleotides that can be introduced, as the enzymes employed can be very selective when it comes to incorporating non-natural substrates, cost, and the necessity of long incubations in some cases. Postsynthetic modification of nucleotides usually consists of the automated synthesis of a short DNA fragment incorporating a specific chemical moiety-usually an amine or a thiol-within or at the termini of the sequence (117,(130)(131)(132). The functionalized oligo is then tagged with the fluorescent probe, which exploits reactions very similar to those employed for the proteins above or listed in Table 2.…”

Section: Polypeptides and Nucleic Acids As Biomolecular Targetsmentioning

confidence: 99%

Fluorescence Spectroscopy: Applications in Chemical Biology

Sapsford

Berti²,

Medintz

2008

Wiley Encyclopedia of Chemical Biology

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Fluorescence spectroscopy in all of its variations can be considered among the most powerful types of analysis available to chemical biology. However, to be useful almost all applications are dependent on optimal labeling of biomolecules with a fluorophore and on the appropriate choice of analytical technique. In this article, we examine the applications and contributions of fluorescent spectroscopy to chemical biology in three inter‐related sections. We first examine the properties of the common fluorophores available from many disparate structural and functional classes, which includes a discussion of their individual benefits and liabilities in the context of their application. The available conjugation chemistries used to attach fluorophores to myriad biomolecules are next reviewed. As each class of biomolecule differs in both structure and function, the focus here is on strategies for the specific labeling of different functional groups. Last, some major types of fluorescent spectroscopy and the associated biologic questions and analysis that can be addressed with them are covered briefly.

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Section: Polypeptides and Nucleic Acids As Biomolecular Targetsmentioning

confidence: 99%

Fluorescence Spectroscopy: Applications in Chemical Biology

Sapsford

Berti²,

Medintz

2008

Wiley Encyclopedia of Chemical Biology

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“…4 ). While two FO residues interfered with STAT3 binding, one could use reactive functional groups on the ODN ends for generating reversible end caps 70 that dissociate after the uptake by live cells thereby abrogating such interference.…”

Section: Discussionmentioning

confidence: 99%

Fluorocarbons Enhance Intracellular Delivery of Short STAT3-sensors and Enable Specific Imaging

Metelev¹,

Zhang²,

Zheng³

et al. 2017

Theranostics

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Short oligonucleotide sequences are now being widely investigated for their potential therapeutic properties. The modification of oligonucleotide termini with short fluorinated residues is capable of drastically altering their behavior in complex in vitro and in vivo systems, and thus may serve to greatly enhance their therapeutic potential. The main goals of our work were to explore: 1) how modification of STAT3 transcription factor-binding oligodeoxynucleotide (ODN) duplexes (ODND) with one or two short fluorocarbon (FC)-based residues would change their properties in vitro and in vivo, and if so, how this would affect their intracellular uptake by cancer cells, and 2) the ability of such modified ODND to form non-covalent complexes with FC-modified carrier macromolecule. The latter has an inherent advantage of producing a 19F-specific magnetic resonance (MR) imaging signature. Thus, we also tested the ability of such copolymers to generate 19F-MR signals.Materials and Methods. Fluorinated nucleic acid residues were incorporated into ODN by using automated synthesis or via activated esters on ODN 5'-ends. To quantify ODND uptake by the cells and to track their stability, we covalently labeled ODN with fluorophores using internucleoside linker technology; the FC-modified carrier was synthesized by acylation of pegylated polylysine graft copolymer with perfluoroundecanoic acid (M5-gPLL-PFUDA).Results. ODN with a single FC group exhibited a tendency to form duplexes with higher melting points and with increased stability against degradation when compared to control non-modified ODNs. ODND carrying fluorinated residues showed complex formation with M5-gPLL-PFUDA as predicted by molecular dynamics simulations. Moreover, FC groups modulated the specificity of ODND binding to the STAT3 target. Finally, FC modification resulted in greater cell uptake (2 to 4 fold higher) when compared to the uptake of non-modified ODND as determined by quantitative confocal fluorescence imaging of A431 and INS-1 cells.Conclusion. ODND modification with FC residues enables fine-tuning of protein binding specificity to double-strand binding motifs and results in an increased internalization by A431 and INS-1 cells in culture. Our results show that modification of ODN termini with FC residues is both a feasible and powerful strategy for developing more efficient nucleic acid-based therapies with the added benefit of allowing for non-invasive MR imaging of ODND therapeutic targeting and response.

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“…The ODN-aldehyde was conjugated to alkaline phosphatase to obtain the ODN-enzyme conjugate that showed unaltered hybridisation properties. Skrzypczynski et al used reductive amination for the ODN conjugation with aminoalkyl-pyrene moiety [65]. Tunitskaya et al prepared ODN containing novel derivative 2'-O-ribofuranosyl-cytidine 63 and oxidised it to dialdehyde group (Fig.…”

Section: Conjugation Via Reductive Amination Hydrazone or Oxime Linkagementioning

confidence: 99%

Chemical Strategies for Oligonucleotide-Conjugates Synthesis

Defrancq

Singh²,

Spinelli

2008

COC

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Oligonucleotide conjugates have found numerous applications in the field of diagnostics and therapeutics. Structurally diverse oligonucleotide conjugates have been prepared and evaluated for various applications. Research efforts have focused on the development of synthetic procedures to accomplish efficient oligonucleotide conjugation with different target molecules. Both on-support and solution-phase coupling procedures have been used to conjugate oligonucleotides. This review gives an account of major synthetic approaches available to prepare covalent oligonucleotide conjugates with diverse target molecules.

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New Reagents for the Introduction of Reactive Functional Groups into Chemically Synthesized DNA Probes

Cited by 15 publications

References 93 publications

Fluorescence Spectroscopy: Applications in Chemical Biology

Fluorescence Spectroscopy: Applications in Chemical Biology

Fluorocarbons Enhance Intracellular Delivery of Short STAT3-sensors and Enable Specific Imaging

Chemical Strategies for Oligonucleotide-Conjugates Synthesis

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