Properties and Anti-HIV Activity of Circular Sense and Antisense Oligonucleotides

Yamakawa, Hidefumi; Ishibashi, Tomoko; Nakashima, Hideki; Yamamoto, Naoki; Takai, Kazuyuki; Takaku, Hiroshi

doi:10.1080/15257779508012551

“…In sharp contrast, L20 started to degrade after 1 hour and completely degraded after 14 hours. This clearly demonstrates these circular DNAs are indeed more stable in biological fluids as is also demonstrated in previous literature [23–25] …”

Section: Figuresupporting

confidence: 85%

“…This clearly demonstrates these circular DNAs are indeed more stable in biological fluids as is also demonstrated in previous literature. [23][24][25] In conclusion, we have developed a highly efficient method for the preparation of ssDNA circles (as short as 16 nts) at high DNA concentrations (100 μM) by introducing a novel design of splint strands. As circular DNA molecules have enhanced chemical stability in biological fluids, we expect that this work could facilitate a wide range of biomedical applications for single-stranded, short nucleic acids.…”

Section: Methodsmentioning

confidence: 99%

“…As circular DNA molecules have enhanced chemical stability in biological fluids, we expect that this work could facilitate a wide range of biomedical applications for single‐stranded, short nucleic acids. For example, they could serve as antisense oligonucleotides for regulation of gene expression and capturing miRNAs [2–4, 23, 24, 26, 27] . They could also be used as a diagnostic tool through miRNA inhibition of smaller sizes [28] or through signal amplification of more specific sequences [11, 12, 29] .…”

Section: Figurementioning

confidence: 99%

See 1 more Smart Citation

Near‐Quantitative Preparation of Short Single‐Stranded DNA Circles

Paluzzi

¹

,

Zhang

²

,

Mao

³

2023

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Small, single-stranded DNA (ssDNA) circles have many applications, such as templating rolling circle amplification (RCA), capturing microRNAs, and scaffolding DNA nanostructures. However, it is challenging to prepare such ssDNA circles, particularly when the DNA size becomes very small (e.g. a 20 nucleotide (nt) long ssDNA circle). Often, such short ssDNA dominantly form concatemers (either linear or circular) due to intermolecular ligation, instead of forming monomeric ssDNA circles by intramolecular ligation. Herein, a simple method to overcome this problem by designing the complementary linker molecules is reported. It is demonstrated that ssDNA, as short as 16 nts, can be enzymatically ligated (by the commonly used T4 DNA ligase) into monomeric ssDNA circles at high concentration (100 μM) with high yield (97 %). This method does not require any special sequence, thus, it is expected to be generally applicable. The experimental protocol is identical to regular DNA ligation, thus, is expected to be user friendly for general chemists and biologists.

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“…At the present time this activity must be investigated on a case‐by‐case basis by using microarrays and cytokine assays, but it is possible that further studies can lead to some general rules to promote, suppress or avoid an inflammatory response by circular aptamers as required. Other nucleic acid therapeutic formats including antisense54, 55 and nucleozyme56 activities are also compatible with a circular DNA format and could be usefully incorporated into suitable constructs in the future. Given the intrinsic problem of combinatorial explosion, realizing the most useful applications of this construct class will require the judicious combination of complementary activities, a task that will be assisted by our improving understanding of target and construct behaviour.…”

Section: Discussionmentioning

confidence: 99%

Multitasking by Multivalent Circular DNA Aptamers

Giusto

¹

,

Knox

²

,

Lai³

et al. 2006

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Nucleic acid aptamers are finding increasing applications in biology, especially as therapeutic candidates and diagnostic components. An important characteristic in meeting the needs of these applications is improved stability in physiological fluids, which is most often accomplished with chemical modification or unnatural nucleotides. In an alternative approach we have specified the design of a multivalent circular DNA aptamer topology that encompasses a number of properties relevant to nucleic acid therapeutic candidates, especially the ability to multitask by combining different activities together within a modular structure. Improved stability in blood products, greater conformational stability, antidoting by complementary circular antiaptamers, heterovalency, transcription factor decoy activity and minimal unintended effects upon the cellular innate immune response are desirable properties that are described here. Multitasking by circular DNA aptamers could similarly find applications in diagnostics and biomaterials, where the combination of interchangeable modules might generate new functions, such as anticoagulation coupled with reversible cell capture as, described here. These results provide a platform for further exploration of multivalent circular aptamer properties, especially in novel combinations of nucleic acid therapeutic modes.

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“…As circular DNA molecules have enhanced chemical stability in biological fluids, we expect that this work could facilitate a wide range of biomedical applications for single‐stranded, short nucleic acids. For example, they could serve as antisense oligonucleotides for regulation of gene expression and capturing miRNAs [2–4, 23, 24, 26, 27] . They could also be used as a diagnostic tool through miRNA inhibition of smaller sizes [28] or through signal amplification of more specific sequences [11, 12, 29] .…”

Section: Figurementioning

confidence: 99%

Near‐Quantitative Preparation of Short Single‐Stranded DNA Circles

Paluzzi

¹

,

Zhang

²

,

Mao

³

2023

Angewandte Chemie

0

View full text Add to dashboard Cite

Small, single-stranded DNA (ssDNA) circles have many applications, such as templating rolling circle amplification (RCA), capturing microRNAs, and scaffolding DNA nanostructures. However, it is challenging to prepare such ssDNA circles, particularly when the DNA size becomes very small (e.g. a 20 nucleotide (nt) long ssDNA circle). Often, such short ssDNA dominantly form concatemers (either linear or circular) due to intermolecular ligation, instead of forming monomeric ssDNA circles by intramolecular ligation. Herein, a simple method to overcome this problem by designing the complementary linker molecules is reported. It is demonstrated that ssDNA, as short as 16 nts, can be enzymatically ligated (by the commonly used T4 DNA ligase) into monomeric ssDNA circles at high concentration (100 μM) with high yield (97 %). This method does not require any special sequence, thus, it is expected to be generally applicable. The experimental protocol is identical to regular DNA ligation, thus, is expected to be user friendly for general chemists and biologists.

show abstract

Properties and Anti-HIV Activity of Circular Sense and Antisense Oligonucleotides

Cited by 6 publications

References 0 publications

Near‐Quantitative Preparation of Short Single‐Stranded DNA Circles

Near‐Quantitative Preparation of Short Single‐Stranded DNA Circles

Multitasking by Multivalent Circular DNA Aptamers

Near‐Quantitative Preparation of Short Single‐Stranded DNA Circles

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