Merging Two Strategies for Mixed-Sequence Recognition of Double-Stranded DNA: Pseudocomplementary Invader Probes

Anderson, Brooke A.; Hrdlicka, Patrick J.

doi:10.1021/acs.joc.6b00369

Cited by 11 publications

(7 citation statements)

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“…26 Recently, we have carried out a series of systematic structure-property studies aiming at improving the dsDNA-recognition efficiency of Invader probes and have thus examined the impact of different nucleobases, 27 relative intercalator orientations, 28 intercalator-sugar linkers, 20 sugar skeletons, 20,29 backbones and probe architectures. 26,30–32 …”

Section: Introductionmentioning

confidence: 99%

Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

et al. 2017

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Development of hybridization-based probes that enable recognition of specific mixed-sequence double-stranded DNA (dsDNA) regions is of considerable interest due to their potential applications in molecular biology, biotechnology, and medicine. We have recently demonstrated that double-stranded probes with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides such as 2′-O-(pyren-1-yl)methyl RNA monomers are inherently activated for recognition of mixed-sequence dsDNA targets, including chromosomal DNA. In the present work, we follow up on our previous structure-activity relationship studies and explore if the dsDNA-recognition efficiency of these so-called Invader probes can be improved by using larger intercalators than pyrene. Oligodeoxyribonucleotides modified with 2′-O-(triphenylen-2-yl)methyl-uridine monomer X and 2′-O-(coronen-1-yl)methyl-uridine monomer Z form extraordinarily stabilized duplexes with complementary DNA (ΔTm’s per modification of up to 13 °C and 20 °C, respectively). Invader probes based on X- and Z-monomers are shown to recognize model dsDNA targets with exceptional binding specificity, but are less efficient than reference probes modified with 2′-O-(pyren-1-yl)methyl-uridine monomer Y. The insight from this study will inform further optimization of Invader probes.

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Section: Introductionmentioning

confidence: 99%

Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

et al. 2017

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“…Hrdlicka and coworkers have introduced so-called Invader probes, i.e., short dsDNA probes that are energetically activated through modification with one or more +1 interstrand zipper arrangements of pyrene-modified nucleotides ( Figure 36 ) [ 17 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 237 , 238 , 239 , 240 ].…”

Section: Agents For Targeting Of Dsdnasmentioning

confidence: 99%

“…Later, various variants of the second generation of dsDNA Invader probes with interstrand zipper arrangements based on 2′-pyrene-modified RNA or DNA monomers were thoroughly studied. They are synthetically more readily accessible and tend to intercalate into DNA duplexes (monomers K , W and Z , i.e., diverse 2′-heteroatoms, linkers, affecting the orientation of intercalator or internucleotidic linkage, Figure 37 ) [ 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 238 , 239 , 240 ].…”

Section: Agents For Targeting Of Dsdnasmentioning

confidence: 99%

“…More recently, the authors of [ 240 ] have suggested to merge two independent strategies for dsDNA targeting, introducing novel pseudocomplementary Invader probes, i.e., chimeras between pseudocomplementary DNA (pcDNA) and Invader probes. These chimeras are energetically activated for mixed-sequence dsDNA recognition through the introduction of pseudocomplementary base pairs (2-thiothymine and 2,6-diaminopurine) and +1 zipper motifs of monomer W1 , respectively.…”

Section: Agents For Targeting Of Dsdnasmentioning

confidence: 99%

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Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

et al. 2017

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In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

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“…Solid-phase synthesis to obtain oligonucleotides of DNA/RNA is a powerful tool that has served several applications in various fields since the 1970s 1,2,3 using phosphoramidite building blocks 4 . Examples of its broad influence include: its impact in labeling (via click chemistry reactions) , source as genetic material 10 , and the study of various natural and/or chemical modifications 11,12 , among many others.The modification that we use here represents the first step in our efforts to obtain RNA oligonucleotides that contain photoactive probes to enable temporal control of structure and function of this important biopolymer.…”

Section: Introductionmentioning

confidence: 99%

Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-<em>O</em>-thiophenylmethyl Modification and Characterization via Circular Dichroism

Francis

Resendiz

2017

JoVE

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Solid-phase synthesis has been used to obtain canonical and modified polymers of nucleic acids, specifically of DNA or RNA, which has made it a popular methodology for applications in various fields and for different research purposes. The procedure described herein focuses on the synthesis, purification, and characterization of dodecamers of RNA 5'-[CUA CGG AAU CAU]-3' containing zero, one, or two modifications located at the C2'-O-position. The probes are based on 2-thiophenylmethyl groups, incorporated into RNA nucleotides via standard organic synthesis and introduced into the corresponding oligonucleotides via their respective phosphoramidites. This report makes use of phosphoramidite chemistry via the four canonical nucleobases (Uridine (U), Cytosine (C), Guanosine (G), Adenosine (A)), as well as 2-thiophenylmethyl functionalized nucleotides modified at the 2'-O-position; however, the methodology is amenable for a large variety of modifications that have been developed over the years. The oligonucleotides were synthesized on a controlled-pore glass (CPG) support followed by cleavage from the resin and deprotection under standard conditions, i.e., a mixture of ammonia and methylamine (AMA) followed by hydrogen fluoride/triethylamine/N-methylpyrrolidinone. The corresponding oligonucleotides were purified via polyacrylamide electrophoresis (20% denaturing) followed by elution, desalting, and isolation via reversed-phase chromatography (Sep-pak, C18-column). Quantification and structural parameters were assessed via ultraviolet-visible (UV-vis) and circular dichroism (CD) photometric analysis, respectively. This report aims to serve as a resource and guide for beginner and expert researchers interested in embarking in this field. It is expected to serve as a work-in-progress as new technologies and methodologies are developed. The description of the methodologies and techniques within this document correspond to a DNA/RNA synthesizer (refurbished and purchased in 2013) that uses phosphoramidite chemistry.

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Merging Two Strategies for Mixed-Sequence Recognition of Double-Stranded DNA: Pseudocomplementary Invader Probes

Cited by 11 publications

References 50 publications

Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-<em>O</em>-thiophenylmethyl Modification and Characterization via Circular Dichroism

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