5V1K

Structure of R-GNA dodecamer

Summary for 5V1K

• Entry DOI: 10.2210/pdb5v1k/pdb
• Descriptor: RNA (5'-R(*CP*GP*CP*GP*AP*AP*(5BU)P*(8RJ)P*AP*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: glycol nucleic acid, gna, rgna, rna, rna x-ray structure, nuclease stability, modified rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 7772.49

Authors

Pallan, P.S.,Egli, M. (deposition date: 2017-03-02, release date: 2017-06-21, Last modification date: 2024-05-22)

Primary citation

Schlegel, M.K.,Foster, D.J.,Kel'in, A.V.,Zlatev, I.,Bisbe, A.,Jayaraman, M.,Lackey, J.G.,Rajeev, K.G.,Charisse, K.,Harp, J.,Pallan, P.S.,Maier, M.A.,Egli, M.,Manoharan, M.
Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA.
J. Am. Chem. Soc., 2017

PubMed Abstract: Here we report the investigation of glycol nucleic acid (GNA), an acyclic nucleic acid analogue, as a modification of siRNA duplexes. We evaluated the impact of (S)- or (R)-GNA nucleotide incorporation on RNA duplex structure by determining three individual crystal structures. These structures indicate that the (S)-nucleotide backbone adopts a conformation that has little impact on the overall duplex structure, while the (R)-nucleotide disrupts the phosphate backbone and hydrogen bonding of an adjacent base pair. In addition, the GNA-T nucleobase adopts a rotated conformation in which the 5-methyl group points into the minor groove, rather than the major groove as in a normal Watson-Crick base pair. This observation of reverse Watson-Crick base pairing is further supported by thermal melting analysis of GNA-C and GNA-G containing duplexes where it was demonstrated that a higher thermal stability was associated with isoguanine and isocytosine base pairing, respectively, over the canonical nucleobases. Furthermore, it was also shown that GNA nucleotide or dinucleotide incorporation increases resistance against snake venom phosphodiesterase. Consistent with the structural data, modification of an siRNA with (S)-GNA resulted in greater in vitro potencies over identical sequences containing (R)-GNA. A walk of (S)-GNA along the guide and passenger strands of a GalNAc conjugate duplex targeting mouse transthyretin (TTR) indicated that GNA is well tolerated in the seed region of both strands in vitro, resulting in an approximate 2-fold improvement in potency. Finally, these conjugate duplexes modified with GNA were capable of maintaining in vivo potency when subcutaneously injected into mice.

PubMed: 28570818
DOI: 10.1021/jacs.7b02694

Experimental method

X-RAY DIFFRACTION (1.18 Å)