Wang G, Vasquez KM (2022) Dynamic alternative DNA structures in biology and disease. Nat Rev Genet. https://doi.org/10.1038/s41576-022-00539-9

Article  PubMed  Google Scholar 

Varshney D, Spiegel J, Zyner K, Tannahill D, Balasubramanian S (2020) The regulation and functions of DNA and RNA G-quadruplexes. Nat Rev Mol Cell Biol 21(8):459–474. https://doi.org/10.1038/s41580-020-0236-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huppert JL, Balasubramanian S (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res 33(9):2908–2916. https://doi.org/10.1093/nar/gki609

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rhodes D, Lipps HJ (2015) G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res 43(18):8627–8637. https://doi.org/10.1093/nar/gkv862

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oh KI, Kim J, Park CJ, Lee JH (2020) Dynamics studies of DNA with non-canonical structure using NMR spectroscopy. Int J Mol Sci 21(8). https://doi.org/10.3390/ijms21082673

Yuan WF, Wan LY, Peng H, Zhong YM, Cai WL, Zhang YQ, Ai WB, Wu JF (2020) The influencing factors and functions of DNA G-quadruplexes. Cell Biochem Funct 38(5):524–532. https://doi.org/10.1002/cbf.3505

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zaccaria F, Paragi G, Fonseca Guerra C (2016) The role of alkali metal cations in the stabilization of guanine quadruplexes: why K(+) is the best. Phys Chem Chem Phys 18(31):20895–20904. https://doi.org/10.1039/c6cp01030j

Article  CAS  PubMed  Google Scholar 

Bhattacharyya D, Mirihana Arachchilage G, Basu S (2016) Metal cations in G-quadruplex folding and stability. Front Chem 4:38. https://doi.org/10.3389/fchem.2016.00038

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jana J, Mohr S, Vianney YM, Weisz K (2021) Structural motifs and intramolecular interactions in non-canonical G-quadruplexes. RSC Chem Biol 2(2):338–353. https://doi.org/10.1039/d0cb00211a

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bugaut A, Balasubramanian S (2008) A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. Biochemistry 47(2):689–697. https://doi.org/10.1021/bi701873c

Article  CAS  PubMed  Google Scholar 

Sahakyan AB, Chambers VS, Marsico G, Santner T, Di Antonio M, Balasubramanian S (2017) Machine learning model for sequence-driven DNA G-quadruplex formation. Sci Rep 7(1):14535. https://doi.org/10.1038/s41598-017-14017-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Agarwala P, Pal G, Pandey S, Maiti S (2017) Mutagenesis reveals an unusual combination of guanines in RNA G-quadruplex formation. ACS Omega 2(8):4790–4799. https://doi.org/10.1021/acsomega.7b00377

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang DH, Fujimoto T, Saxena S, Yu HQ, Miyoshi D, Sugimoto N (2010) Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors. Biochemistry 49(21):4554–4563. https://doi.org/10.1021/bi1002822

Article  CAS  PubMed  Google Scholar 

Kankia B (2019) Stability factors of the parallel quadruplexes: DNA versus RNA. J Phys Chem B 123(5):1060–1067. https://doi.org/10.1021/acs.jpcb.8b11559

Article  CAS  PubMed  Google Scholar 

Xiao CD, Shibata T, Yamamoto Y, Xu Y (2018) An intramolecular antiparallel G-quadruplex formed by human telomere RNA. Chem Commun (Camb) 54(32):3944–3946. https://doi.org/10.1039/c8cc01427b

Article  CAS  PubMed  Google Scholar 

Xiao CD, Ishizuka T, Xu Y (2017) Antiparallel RNA G-quadruplex formed by human telomere RNA containing 8-bromoguanosine. Sci Rep 7(1):6695. https://doi.org/10.1038/s41598-017-07050-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Banco MT, Ferré-D’Amaré AR (2021) The emerging structural complexity of G-quadruplex RNAs. RNA 27(4):390–402. https://doi.org/10.1261/rna.078238.120

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yu H, Qi Y, Yang B, Yang X, Ding Y (2023) G4Atlas: a comprehensive transcriptome-wide G-quadruplex database. Nucleic Acids Res 51(D1):D126-d134. https://doi.org/10.1093/nar/gkac896

Article  PubMed  Google Scholar 

Lyu K, Chow EY, Mou X, Chan TF, Kwok CK (2021) RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res 49(10):5426–5450. https://doi.org/10.1093/nar/gkab187

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ransohoff JD, Wei Y, Khavari PA (2018) The functions and unique features of long intergenic non-coding RNA. Nat Rev Mol Cell Biol 19(3):143–157. https://doi.org/10.1038/nrm.2017.104

Article  CAS  PubMed  Google Scholar 

Cech TR, Steitz JA (2014) The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157(1):77–94. https://doi.org/10.1016/j.cell.2014.03.008

Article  CAS  PubMed  Google Scholar 

Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM (2019) The roles of structural dynamics in the cellular functions of RNAs. Nat Rev Mol Cell Biol 20(8):474–489. https://doi.org/10.1038/s41580-019-0136-0

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tassinari M, Richter SN, Gandellini P (2021) Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome. Nucleic Acids Res 49(7):3617–3633. https://doi.org/10.1093/nar/gkab127

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kopp F, Mendell JT (2018) Functional classification and experimental dissection of long noncoding RNAs. Cell 172(3):393–407. https://doi.org/10.1016/j.cell.2018.01.011

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311–1323. https://doi.org/10.1016/j.cell.2007.05.022

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA et al (2014) LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. Mol Cell 54(5):777–790. https://doi.org/10.1016/j.molcel.2014.04.025

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA et al (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39(6):925–938. https://doi.org/10.1016/j.molcel.2010.08.011

Article  CAS  PubMed  PubMed Central  Google Scholar 

Su K, Wang N, Shao Q, Liu H, Zhao B, Ma S (2021) The role of a ceRNA regulatory network based on lncRNA MALAT1 site in cancer progression. Biomed Pharmacother 137:111389. https://doi.org/10.1016/j.biopha.2021.111389

Johnsson P, Lipovich L, Grandér D, Morris KV (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta 1840(3):1063–1071. https://doi.org/10.1016/j.bbagen.2013.10.035

Article  CAS  PubMed  Google Scholar 

Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147(7):1537–1550. https://doi.org/10.1016/j.cell.2011.11.055

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10(3):155–159. https://doi.org/10.1038/nrg2521

Article  CAS  PubMed  Google Scholar 

Pang KC, Frith MC, Mattick JS (2006) Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 22(1):1–5. https://doi.org/10.1016/j.tig.2005.10.003

Article  CAS  PubMed  Google Scholar 

Smith MA, Gesell T, Stadler PF, Mattick JS (2013) Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res 41(17):8220–8236. https://doi.org/10.1093/nar/gkt596

Article  CAS  PubMed  PubMed Central  Google Scholar 

Diederichs S (2014) The four dimensions of noncoding RNA conservation. Trends Genet 30(4):121–123. https://doi.org/10.1016/j.tig.2014.01.004

Article  CAS  PubMed  Google Scholar 

Jayaraj GG, Pandey S, Scaria V, Maiti S (2012) Potential G-quadruplexes in the human long non-coding transcriptome. RNA Biol 9(1):81–86. https://doi.org/10.4161/rna.9.1.18047

Article  CAS