Base‐Pairing Properties of a Structural Isomer of Glycerol Nucleic Acid

Karri, Phaneendrasai; Punna, Venkateshwarlu; Kim, Keun Soo; Krishnamurthy, Ramanarayanan

doi:10.1002/ange.201300795

Cited by 11 publications

(4 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The siRNA duplex showed increased optical density from 1.53 to 2.27 at 190 nm and from 0.24 and 0.28 at 260 nm upon increasing the temperature from 20 to 90 °C, and PAMAM-ND/siRNA (1:1 ratio) complexes showed a similar tendency in optical density, compared to the bare siRNA duplex (from 2.07 to 3.04 at 190 nm and from 0.28 to 0.33 at 260 nm). The hyperchromicity of UV absorbance at 260 nm resulted from unwinding the double stranded siRNA, forming single-stranded RNA, and unstacking siRNA as the temperature ramped up . Specifically, PAMAM-ND/siRNA with 2:1 ratio complexes showed optical density changes from 1.39 to 2.21 at 190 nm and from 0.03 to 0.03 at 260 nm.…”

Section: Resultsmentioning

confidence: 99%

Polyamidoamine-Decorated Nanodiamonds as a Hybrid Gene Delivery Vector and siRNA Structural Characterization at the Charged Interfaces

Lim

Rajasekaran

Lee

et al. 2017

ACS Appl. Mater. Interfaces

View full text Add to dashboard Cite

Nanodiamonds have been discovered as a new exogenous material source in biomedical applications. As a new potent form of nanodiamond (ND), polyamidoamine-decorated nanodiamonds (PAMAM-NDs) were prepared for E7 or E6 oncoprotein-suppressing siRNA gene delivery for high risk human papillomavirus-induced cervical cancer, such as types 16 and 18. It is critical to understand the physicochemical properties of siRNA complexes immobilized on cationic solid ND surfaces in the aspect of biomolecular structural and conformational changes, as the new inert carbon material can be extended into the application of a gene delivery vector. A spectral study of siRNA/PAMAM-ND complexes using differential scanning calorimetry and circular dichroism spectroscopy proved that the hydrogen bonding and electrostatic interactions between siRNA and PAMAM-NDs decreased endothermic heat capacity. Moreover, siRNA/PAMAM-ND complexes showed low cell cytotoxicity and significant suppressing effects for forward target E6 and E7 oncogenic genes, proving functional and therapeutic efficacy. The cellular uptake of siRNA/PAMAM-ND complexes at 8 h was visualized by macropinocytes and direct endosomal escape of the siRNA/PAMAM-ND complexes. It is presumed that PAMAM-NDs provided a buffering cushion to adjust the pH and hard mechanical stress to escape endosomes. siRNA/PAMAM-ND complexes provide a potential organic/inorganic hybrid material source for gene delivery carriers.

show abstract

Section: Resultsmentioning

confidence: 99%

Polyamidoamine-Decorated Nanodiamonds as a Hybrid Gene Delivery Vector and siRNA Structural Characterization at the Charged Interfaces

Lim

Rajasekaran

Lee

et al. 2017

ACS Appl. Mater. Interfaces

View full text Add to dashboard Cite

show abstract

“…Such a disposition in the (1′→3′)‐linked pentulofuranosyl NA systems results in a pronounced decrease in the interstrand phosphodiester distance (Figure 7 a/c). The rigidity of the cyclic system prevents any adjustments to minimize this interaction, thus intensifying the electrostatic repulsion and hindering duplex formation 26. The ramification of such an organization is that the (1′→3′)‐linked NA in the pentulofuranosyl series would not give rise to a pairing system irrespective of what the configuration (α or β) at the anomeric center is 25.…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, the pentulose NA systems, which also have the ‘same number of atoms’ as RNA and p ‐RNA, are devoid of base pairing; here, the major factors are that the nucleobase and the phosphates (unlike RNA and p ‐RNA) are now on the same side of the sugar unit leading to a shortened interstrand distance between the phosphate groups (Figure 7 c). This arrangement, in combination with the rigid furanosyl structure, seems to prevent any accommodations towards a base‐paring conformation, which would require an energetically unfavorable syn nucleobase conformation 26…”

Section: Discussionmentioning

confidence: 99%

“…Here, a good base‐pairing system (RNA) is converted into a poor‐base‐pairing system (FNA) by the deletion of the pentofuranose ring structure (Figure 8 a and 8 b). On the other hand, removing the pentulofuranosyl ring structure from the pentulose NA (a system with no base pairing) gives rise to a structural isomer of glycerol nucleic acid (iso‐GNA), which is now a better base‐pairing system26 compared to its parent (Figure 8 c and 8 d). This dichotomous effect of the removal of the ring structure on the base‐pairing properties of pentose NA and pentulose NA highlights the role the ring structure plays in determining the base‐pairing propensity of the canonical nucleobases.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Chemical Etiology of Nucleic Acid Structure: The Pentulofuranosyl Oligonucleotide Systems: The (1′→3′)‐β‐L‐Ribulo, (4′→3′)‐α‐L‐Xylulo, and (1′→3′)‐α‐L‐Xylulo Nucleic Acids

Stoop

Meher

Karri

et al. 2013

Chemistry A European J

Self Cite

View full text Add to dashboard Cite

Under potentially prebiotic scenarios, ribose (pentose), the component of RNA is formed in meager amounts, as opposed to ribulose and xylulose (pentuloses). Consequently, replacement of ribose in RNA, with pentulose sugars, gives rise to prospective oligonucleotide candidates that are potentially prebiotic structural variants of RNA that could be formed by the same type of chemical pathways that gave rise to RNA from ribose. The potentially natural alternative (1'→3')-ribulo oligonucleotides and (4'→3')- and (1'→3')-xylulo oligonucleotides consisting of adenine and thymine were synthesized and found to exhibit no self-pairing or cross-pairing with RNA. This signifies that even though pentulose sugars may have been abundant in a prebiotic scenario, the pentulose nucleic acids (NAs), if and when formed, would not have been competitors of RNA, or interfered with the emergence of RNA as a functional informational system. The reason for the lack of base pairing in pentulose NA highlights the contrasting and central role played by the furanosyl ring in RNA and pentulose NA, enabling and optimizing the base pairing in RNA, while impeding it in pentulose NA.

show abstract

Synthesis of Triazole‐linked Homonucleoside Polymers through Topochemical Azide–Alkyne Cycloaddition

Pathigoolla

Sureshan

2014

Angewandte Chemie

View full text Add to dashboard Cite

There is a great deal of interest in developing stable modified nucleic acids for application in diverse fields. Phosphate-modified DNA analogues, in which the phosphodiester group is replaced with a surrogate group, are attractive because of their high stability and resistance to nucleases. However, the scope of conventional solution or solid-phase DNA synthesis is limited for making DNA analogues with unnatural linkages. Other limitations associated with conventional synthesis include difficulty in making larger polymers, poor yield, incomplete reaction, and difficult purification. To circumvent these problems, a single-crystal-to-single-crystal (SCSC) synthesis of a 1,5-triazole-linked polymeric ssDNA analogue from a modified nucleoside through topochemical azide-alkyne cycloaddition (TAAC) is reported. This is the first solvent-free, catalyst-free synthesis of a DNA analogue that proceeds in quantitative yield and does not require any purification.

show abstract

Base‐Pairing Properties of a Structural Isomer of Glycerol Nucleic Acid

Cited by 11 publications

References 39 publications

Polyamidoamine-Decorated Nanodiamonds as a Hybrid Gene Delivery Vector and siRNA Structural Characterization at the Charged Interfaces

Polyamidoamine-Decorated Nanodiamonds as a Hybrid Gene Delivery Vector and siRNA Structural Characterization at the Charged Interfaces

Chemical Etiology of Nucleic Acid Structure: The Pentulofuranosyl Oligonucleotide Systems: The (1′→3′)‐β‐L‐Ribulo, (4′→3′)‐α‐L‐Xylulo, and (1′→3′)‐α‐L‐Xylulo Nucleic Acids

Synthesis of Triazole‐linked Homonucleoside Polymers through Topochemical Azide–Alkyne Cycloaddition

Contact Info

Product

Resources

About