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1. Filament assembly underpins the double-stranded DNA specificity of AIM2-like receptors

   https://doi.org/10.1093/nar/gkad090  

   Garg, Archit ; Stallings, Christina M. ; Sohn, Jungsan ( March 2023 , Nucleic Acids Research)

   Upon sensing cytosolic- and/or viral double-stranded (ds)DNA, absent-in-melanoma-2 (AIM2)-like-receptors (ALRs) assemble into filamentous signaling platforms to initiate inflammatory responses. The versatile yet critical roles of ALRs in host innate defense are increasingly appreciated; however, the mechanisms by which AIM2 and its related IFI16 specifically recognize dsDNA over other nucleic acids remain poorly understood (i.e. single-stranded (ss)DNA, dsRNA, ssRNA and DNA:RNA hybrid). Here, we find that although AIM2 can interact with various nucleic acids, it preferentially binds to and assembles filaments faster on dsDNA in a duplex length-dependent manner. Moreover, AIM2 oligomers assembled on nucleic acids other than dsDNA not only display less ordered filamentous structures, but also fail to induce the polymerization of downstream ASC. Likewise, although showing broader nucleic acid selectivity than AIM2, IFI16 binds to and oligomerizes most readily on dsDNA in a duplex length-dependent manner. Nevertheless, IFI16 fails to form filaments on single-stranded nucleic acids and does not accelerate the polymerization of ASC regardless of bound nucleic acids. Together, we reveal that filament assembly is integral to nucleic acid distinction by ALRs.

    

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2. Concurrent Prebiotic Formation of Nucleoside‐Amidophosphates and Nucleoside‐Triphosphates Potentiates Transition from Abiotic to Biotic Polymerization

   https://doi.org/10.1002/ange.202113625  

   Lin, Huacan ; Jiménez, Eddy I. ; Arriola, Joshua T. ; Müller, Ulrich F. ; Krishnamurthy, Ramanarayanan ( November 2021 , Angewandte Chemie)

   Polymerization of nucleic acids in biology utilizes 5′‐nucleoside triphosphates (NTPs) as substrates. The prebiotic availability of NTPs has been unresolved and other derivatives of nucleoside‐monophosphates (NMPs) have been studied. However, this latter approach necessitates a change in chemistries when transitioning to biology. Herein we show that diamidophosphate (DAP), in a one‐pot amidophosphorylation‐hydrolysis setting converts NMPs into the corresponding NTPs via 5′‐nucleoside amidophosphates (NaPs). The resulting crude mixture of NTPs are accepted by proteinaceous‐ and ribozyme‐polymerases as substrates for nucleic acid polymerization. This phosphorylation also operates at the level of oligonucleotides enabling ribozyme‐mediated ligation. This one‐pot protocol for simultaneous generation of NaPs and NTPs suggests that the transition from prebiotic‐phosphorylation and oligomerization to an enzymatic processive‐polymerization can be more continuous than previously anticipated.

    

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3. Concurrent Prebiotic Formation of Nucleoside‐Amidophosphates and Nucleoside‐Triphosphates Potentiates Transition from Abiotic to Biotic Polymerization

   https://doi.org/10.1002/anie.202113625  

   Lin, Huacan ; Jiménez, Eddy I. ; Arriola, Joshua T. ; Müller, Ulrich F. ; Krishnamurthy, Ramanarayanan ( November 2021 , Angewandte Chemie International Edition)

   Polymerization of nucleic acids in biology utilizes 5′‐nucleoside triphosphates (NTPs) as substrates. The prebiotic availability of NTPs has been unresolved and other derivatives of nucleoside‐monophosphates (NMPs) have been studied. However, this latter approach necessitates a change in chemistries when transitioning to biology. Herein we show that diamidophosphate (DAP), in a one‐pot amidophosphorylation‐hydrolysis setting converts NMPs into the corresponding NTPs via 5′‐nucleoside amidophosphates (NaPs). The resulting crude mixture of NTPs are accepted by proteinaceous‐ and ribozyme‐polymerases as substrates for nucleic acid polymerization. This phosphorylation also operates at the level of oligonucleotides enabling ribozyme‐mediated ligation. This one‐pot protocol for simultaneous generation of NaPs and NTPs suggests that the transition from prebiotic‐phosphorylation and oligomerization to an enzymatic processive‐polymerization can be more continuous than previously anticipated.

    

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4. Peptide nucleic acids harness dual information codes in a single molecule

   https://doi.org/10.1039/C9CC09905K  

   Swenson, Colin S. ; Heemstra, Jennifer M. ( February 2020 , Chemical Communications)

   Nature encodes the information required for life in two fundamental biopolymers: nucleic acids and proteins. Peptide nucleic acid (PNA), a synthetic analog comprised of nucleobases arrayed along a pseudopeptide backbone, has the ability to combine the power of nucleic acids to encode information with the versatility of amino acids to encode structure and function. Historically, PNA has been perceived as a simple nucleic acid mimic having desirable properties such as high biostability and strong affinity for complementary nucleic acids. In this feature article, we aim to adjust this perception by highlighting the ability of PNA to act as a peptide mimic and showing the largely untapped potential to encode information in the amino acid sequence. First, we provide an introduction to PNA and discuss the use of conjugation to impart tunable properties to the biopolymer. Next, we describe the integration of functional groups directly into the PNA backbone to impart specific physical properties. Lastly, we highlight the use of these integrated amino acid side chains to encode peptide-like sequences in the PNA backbone, imparting novel activity and function and demonstrating the ability of PNA to simultaneously mimic both a peptide and a nucleic acid. 

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5. Stimuli-responsive assembly of bilingual peptide nucleic acids

   https://doi.org/10.1039/D2CB00020B  

   Argueta-Gonzalez, Hector S. ; Swenson, Colin S. ; Song, George ; Heemstra, Jennifer M. ( June 2022 , RSC Chemical Biology)

   Peptide nucleic acids (PNAs) are high-affinity synthetic nucleic acid analogs capable of hybridization with native nucleic acids. PNAs synthesized having amino acid sidechains installed at the γ-position along the backbone provide a template for a single biopolymer to simultaneously encode nucleic acid and amino acid sequences. Previously, we reported the development of “bilingual” PNAs through the synthesis of an amphiphilic sequence featuring separate blocks of hydrophobic and hydrophilic amino acid functional groups. These PNAs combined the sequence-specific binding activity of nucleic acids with the structural organization properties of peptides. Like other amphiphilic compounds, these γ-PNAs were observed to assemble spontaneously into micelle-like nanostructures in aqueous solutions and disassembly was induced through hybridization to a complementary sequence. Here, we explore whether assembly of these bilingual PNAs is possible by harnessing the nucleic acid code. Specifically, we designed an amphiphile-masking duplex system in which spontaneous amphiphile assembly is prevented through hybridization to a nucleic acid masking sequence. We show that the amphiphile is displaced upon introduction of a releasing sequence complementary to the masking sequence through toehold mediated displacement. Upon release, we observe that the amphiphile proceeds to assemble in a fashion consistent with our previously reported structures. Our approach represents a novel method for controlled stimuli-responsive assembly of PNA-based nanostructures. 

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