1H, 13C, and 15N chemical shift assignments of a G-quadruplex forming sequence within the KRAS proto-oncogene promoter region

Abstract

Single stranded guanine rich DNA (or RNA) sequences adopt noncanonical secondary structures called G-quadruplexes (G4). Functionally, quadruplexes control gene transcription and regulate activities such as replication, gene recombination or alternative splicing. Hence they are potential targets for cancer, neuronal, and viral related diseases. KRAS is one of the most mutated oncogenes in the genome of cancer cells and contains a nuclease hypersensitive element (NHE) sequence capable of forming G-quadruplexes via its six runs of guanines. In our work, we are interested in the NMR structure of the major G4 scaffold formed in the KRAS NHE region with a mutated sequence of 22 residues. Here, we report H,C and N chemical shift assignments the G4 formed within KRAS22RT sequence.

The Promoter Region of the Proto-Oncogene MST1R Contains the Main Features of G-Quadruplexes Formation

“…Above a score of 1.5, the sequences tend to form a stable G4 as described elsewhere [ 22 ]. Usually, the stability protocols are performed at 25 °C, and in some cases structures are reported stable at temperatures as high as 37 °C [ 23 ].…”

“…It would therefore be interesting to study each of MST1R G4 sequences in detail and obtain further 2D and 3D structural data for the most relevant structures obtained from a complete set of polymerase stop and cellular viability assays. A detailed study would allow to compare results with other cases where G4 structures are present in oncogene promoter regions such as KRAS [ 17 , 18 , 23 ] or c-MYC [ 20 ], and thus better understand their potential role in transcription regulation. Additional studies where several G4 ligand families could be tested against the abovementioned sequences would also be interesting for comparative studies, having in mind possible therapeutic purposes [ 27 , 28 ].…”

G4-iM Grinder: DNA and RNA G-Quadruplex, i-Motif and higher order structure search and analyser tool

“…For the most part, variable configuration is usually heavily restricted meaning only the same kind of structures can be looked for (Table 1), excluding -for examplethe detection of structures with more than four G-runs in the sequence. Even if only four G-runs can form the G4-tetrads, extra G-runs can also occur in G-quadruplexes (19,20) or as part of a fluctuating structure (21). Additionally, no current search engine considers nor calculates genomic PQS frequency from the results.…”

Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses

“…The structure of RG-1 was predicted from a multiple sequence alignment with three DNA G4 sequences corresponding to experimental structures (PDB codes 2N4Y, 24 6T51, 25 5I2V). 26 The RG-1 structural model exhibits a parallel G4 composed of two superposed tetrads (see Figure 1 ).…”