Introducing LNAzo: More Rigidity for Improved Photocontrol of Oligonucleotide Hybridization**

Abstract

Oligonucleotide-based therapeutics have made rapid progress in clinical treatment of av ariety of disease indications. Since most therapeutic oligonucleotides serve more than just one functiona nd tend to have ap rolonged lifetime, spatio-temporal control of these functions would be desirable. Photoswitches like azobenzene have proven themselves as useful tools in this matter.U pon irradiation, the photoisomerization of the azobenzene moiety causes destabilization in adjacent base pairs, leading to ad ecreased hybridizationa ffinity.S ince the way the azobenzene is incorporated in the oligonucleotide is of utmosti mportance,w es ynthesized locked azobenzene Cnucleosides and compared their photocontrol capabilities to established azobenzene C-nucleosides in oligonucleotide test-sequences by meanso ff luorescence-, UV/Vis-, and CD-spectroscopy.Artificialc ontrol of biological functionr emains one of the most importantt opics of oligonucleotide chemistry.I nl iving organisms, oligonucleotide hybridization regulates the expression of genes and biosynthesis by revealing the encoded information only when desired. The simple base-pairingr ules led to many promisinga pplicationsin cell biology,p harmacology,o rn anotechnology. [1][2][3][4][5][6] For instance, oligonucleotide therapeutics against miRNA-34a play am ajor role in controlling cell proliferation. [7] However,m iRNA-34a is an important tumor suppressor and correspondinga ntimiRs have been shown to causes erious adversee ffects in off-target tissues in clinicalt rials [8] and have an in vivo half-life time of up to several weeks. [9] The need for ac onvenient method to add spatio-temporal control to therapeutic oligonucleotides led to many studies regardingt he distribution, cell uptake, and pharmacokinetics. [10][11][12] Ap ossible way of gainingc ontrol over these effects is the incorporationo fl ight-responsive elements. In contrast to most chemical stimuli, light does not pollute the system, is harmless for biological applicationsa nd can be applied with high spatio-temporalc ontrola nd dose-precision. [13][14][15] Several examples of photoactivatablea ntimiRs have been synthesized utilizing photocleavable protecting groups. [16,17] Unfortunately, activation of antimiRs with photocleavable protecting groups is an irreversible process;t herefore, adverse effects need to be taken into consideration. To harness the energy of light and translate it into ar eversible reaction, ar eversible system, which can be switched between different states,i sd esirable. Photoswitchesl ike spiropyrans, [18,19] hemithioindigos, [20] rhodopsins [21] or azobenzenes [22,23] can isomerize into different isoforms when irradiated with light of corresponding wavelength.Azobenzenes have ag reat potentialf or oligonucleotide applications.T hey are easy to synthesize, [24] can be custom tailored to the applications requirements, [25] and have already been used in numerous studies involving oligonucleotides. [22,26] Azobenzenes have two distinct photoisomers. The trans state azobenzene i...

Photoswitchable 2‐Phenyldiazenyl‐Purines and their Influence on DNA Hybridization

“…In addition, the azobenzene needs to be positioned in the base pair stack without the possibility to evade into the minor or major groove during isomerization. Replacing nucleobases with azobenzenes to create azobenzene C ‐nucleosides does exactly that and has been shown to regulate hybridization in DNA, RNA and DNA‐nanostructures [24–27] . Apparently, introducing azobenzene as a nucleobase substitute implies a steric disturbance in the duplex even in the favored trans ‐state, which results in decreased binding affinity.…”

“…Replacing nucleobases with azobenzenes to create azobenzene C-nucleosides does exactly that and has been shown to regulate hybridization in DNA, RNA and DNAnanostructures. [24][25][26][27] Apparently, introducing azobenzene as a nucleobase substitute implies a steric disturbance in the duplex even in the favored trans-state, which results in decreased binding affinity.…”

Light switching for product selectivity control in photocatalysis

“…42 This photoisomerization leads to a change in the properties of the molecule, including its geometry and hence spatial-steric properties and molecule rigidity that can all influence reactivity, changed electronic properties, basicity, etc. [57][58][59][60][61] Some remarkable progress has been made via the incorporation of photo responsive units within the structure of the active catalyst. For these catalyst systems, an external stimulus can change their intrinsic catalytic activity, which is subsequently translated to an alteration of the rate of a specific reaction, or to switch it ON/OFF, or generate a completely different product outcome.…”

Chemo-enzymatische Synthese lichtaktivierbarer RNA & Synthese lichtregulierbarer Oligonukleotide zur spektroskopischen Strukturaufklärung

“…[49,317] Zusätzlich wurde von Grebenovsky et al 2019 ein LNA-basiertes C-Nukleosid vorgestellt (LNAzo-C-Nukleosid). [318] Bemerkenswert ist die gute Effizienz der trans/cis-Isomerisierung von bis zu 98% bei Bestrahlung mit 365 nm bei Raumtemperatur. [49,317] Damit beeinflussen Azobenzol-C-Nukleoside die Duplexstabilität deutlich besser, als der azyklische D-Threoninol-Linker (tAzo, Abb.…”

“…Goldau et al präsentierten 2015 meta-und para-subsituierte Azobenzol-C-Nukleoside (mAzo-und pAzo-C-Nukleosid) zur reversiblen Regulierung der DNA-und auch RNA-Hybridisierung [49,317]. Zusätzlich wurde von Grebenovsky et al 2019 ein LNA-basiertes C-Nukleosid vorgestellt (LNAzo-C-Nukleosid) [318]. Bemerkenswert ist die gute Effizienz der trans/cis-Isomerisierung von bis zu 98% bei Bestrahlung mit 365 nm bei Raumtemperatur [49,317].…”