Skip to main content
SpringerLink
Log in

Stability Prediction of Canonical and Noncanonical Structures of Nucleic Acids

  • Living reference work entry
  • First Online:
Handbook of Chemical Biology of Nucleic Acids

  • 96 Accesses

Abstract

The folding and unfolding of nucleic acids (DNA and RNA) is essential for cellular functions. These structural changes in nucleic acids are also widely used in various technical applications using nucleic acids. Thermodynamics for the structural changes is highly useful and important for understanding the biological mechanism of nucleic acid function, as well as for the design of materials for nucleic acids. The canonical structure of nucleic acids is a duplex comprising of Watson-Crick base pairs. As the thermodynamic properties of nucleic acid structures depend on the chemical interactions between nucleotides in the strands, the stability of the duplex can be determined by the sequence, which indicates that stability is predictable. In fact, the stability prediction of nucleic acid duplexes has been developed and widely used. However, such predictions cannot always be adopted in various solution conditions, especially cellular conditions, as the concentrations of cations and co-solutes in the intracellular condition, termed molecular crowding, vary from those under standard experimental conditions. In addition, the crowding conditions in cells are spatiotemporally variable. Furthermore, there are noncanonical structures that are different from duplexes, such as triplexes and tetraplexes. Therefore, there is a need for a method to predict the stability of various nucleic acid structures under cellular conditions. This chapter guides readers through the study of the physicochemical basis for predicting nucleic acid stability and discusses recent studies on the prediction of stability in cellular conditions.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  • Adams MS, Znosko BM (2019) Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions. Nucleic Acids Res 47:3658–3666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Allawi HT, SantaLucia Jr J (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36:10581–10594

    Article  CAS  PubMed  Google Scholar 

  • Allawi HT, SantaLucia Jr J (1998a) Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. Biochemistry 37:2170–2179

    Article  CAS  PubMed  Google Scholar 

  • Allawi HT, SantaLucia Jr J (1998b) Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. Biochemistry 37:9435–9444

    Article  CAS  PubMed  Google Scholar 

  • Allawi HT, SantaLucia Jr J (1998c) Thermodynamics of internal C.T mismatches in DNA. Nucleic Acids Res 26:2694–2701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Antao VP, Lai SY, Tinoco Jr I (1991) A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res 19:5901–5905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Banerjee D, Tateishi-Karimata H, Ghosh S, Ohyama T, Endoh T, Takahashi S, Sugimoto N (2020a) Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition. Nucleic Acids Res

    Google Scholar 

  • Banerjee D, Tateishi-Karimata H, Ohyama T, Ghosh S, Endoh T, Takahashi S, Sugimoto N (2020b) Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition. Nucleic Acids Res 48:12042–12054

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Banerjee D, Tateishi-Karimata H, Ohyama T, Ghosh S, Endoh T, Takahashi S, Sugimoto N (2021) Correction to ‘Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition’. Nucleic Acids Res 49:10796–10799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Basilio Barbosa V, de Oliveira Martins E, Weber G (2019) Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations. Biophys Chem 251:106189

    Article  CAS  PubMed  Google Scholar 

  • Belmonte-Reche E, Morales JC (2019) G4-iM Grinder: when size and frequency matter. G-quadruplex, i-Motif and higher order structure search and analysis tool. NAR Genom Bioinform 2:lqz005

    Article  PubMed  PubMed Central  Google Scholar 

  • Bhavsar-Jog YP, Van Dornshuld E, Brooks TA, Tschumper GS, Wadkins RM (2014) Epigenetic modification, dehydration, and molecular crowding effects on the thermodynamics of i-motif structure formation from C-rich DNA. Biochemistry 53:1586–1594

    Article  CAS  PubMed  Google Scholar 

  • Bommarito S, Peyret N, SantaLucia Jr J (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res 28:1929–1934

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Booher MA, Wang S, Kool ET (1994) Base pairing and steric interactions between pyrimidine strand bridging loops and the purine strand in DNA pyrimidine.purine.pyrimidine triplexes. Biochemistry 33:4645–4651

    Article  CAS  PubMed  Google Scholar 

  • Brazier JA, Shah A, Brown GD (2012) I-Motif formation in gene promoters: unusually stable formation in sequences complementary to known G-quadruplexes. Chem Commun 48:10739–10741

    Article  CAS  Google Scholar 

  • Breslauer KJ, Frank R, Blocker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A 83:3746–3750

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Y, Agrawal P, Brown RV, Hatzakis E, Hurley L, Yang D (2012) The major G-quadruplex formed in the human platelet-derived growth factor receptor beta promoter adopts a novel broken-strand structure in K+ solution. J Am Chem Soc 134:13220–13223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng M, Cheng Y, Hao J, Jia G, Zhou J, Mergny JL, Li C (2018) Loop permutation affects the topology and stability of G-quadruplexes. Nucleic Acids Res 46:9264–9275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng M, Qiu D, Tamon L, Ištvánková E, Víšková P, Amrane S, Guédin A, Chen J, Lacroix L, Ju H et al (2021) Thermal and pH stabilities of i-DNA: confronting in vitro experiments with models and In-Cell NMR data. Angew Chem Int Ed 60:10286–10294

    Article  CAS  Google Scholar 

  • Crothers DM, Bloomfield VA, Tinoco I (2000) Nucleic acids: structures, properties. and functions (University science books)

    Google Scholar 

  • Dettler JM, Buscaglia R, Cui J, Cashman D, Blynn M, Lewis EA (2010) Biophysical characterization of an ensemble of intramolecular i-motifs formed by the human c-MYC NHE III1 P1 promoter mutant sequence. Biophys J 99:561–567

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505:696–700

    Article  CAS  PubMed  Google Scholar 

  • Dvorkin SA, Karsisiotis AI, Webba da Silva M (2018) Encoding canonical DNA quadruplex structure. Sci Adv 4:eaat3007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ferreira I, Jolley EA, Znosko BM, Weber G (2019) Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters. Chem Phys 521:69–76

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fleming AM, Ding Y, Rogers RA, Zhu J, Zhu J, Burton AD, Carlisle CB, Burrows CJ (2017) 4n-1 Is a “Sweet Spot” in DNA i-Motif Folding of 2′-Deoxycytidine Homopolymers. J Am Chem Soc 139:4682–4689

    Article  CAS  PubMed  Google Scholar 

  • Fleming AM, Stewart KM, Eyring GM, Ball TE, Burrows CJ (2018) Unraveling the 4n – 1 rule for DNA i-motif stability: base pairs vs. loop lengths. Org Biomol Chem 16:4537–4546

    Article  CAS  PubMed  Google Scholar 

  • Freier SM, Alkema D, Sinclair A, Neilson T, Turner DH (1985) Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry 24:4533–4539

    Article  CAS  PubMed  Google Scholar 

  • Freier SM, Kierzek R, Caruthers MH, Neilson T, Turner DH (1986a) Free energy contributions of G.U and other terminal mismatches to helix stability. Biochemistry 25:3209–3213

    Article  CAS  PubMed  Google Scholar 

  • Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH (1986b) Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A 83:9373–9377

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fujii T, Sugimoto N (2015) Loop nucleotides impact the stability of intrastrand i-motif structures at neutral pH. Phys Chem Chem Phys 17:16719–16722

    Article  CAS  PubMed  Google Scholar 

  • Ghosh S, Takahashi S, Endoh T, Tateishi-Karimata H, Hazra S, Sugimoto N (2019) Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition. Nucleic Acids Res 47:3284–3294

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghosh S, Takahashi S, Ohyama T, Endoh T, Tateishi-Karimata H, Sugimoto N (2020) Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions. Proc Natl Acad Sci U S A 117:14194–14201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gorodkin J, Ruzzo WL (2014) RNA sequence, structure, and function: computational and bioinformatic methods. Springer

    Book  Google Scholar 

  • Gurung SP, Schwarz C, Hall JP, Cardin CJ, Brazier JA (2015) The importance of loop length on the stability of i-motif structures. Chem Commun 51:5630–5632

    Article  CAS  Google Scholar 

  • Hazel P, Huppert J, Balasubramanian S, Neidle S (2004) Loop-length-dependent folding of G-quadruplexes. J Am Chem Soc 126:16405–16415

    Article  CAS  PubMed  Google Scholar 

  • Hickey DR, Turner DH (1985) Effects of terminal mismatches on RNA stability: thermodynamics of duplex formation for ACCGGGp, ACCGGAp, and ACCGGCp. Biochemistry 24:3987–3991

    Article  CAS  PubMed  Google Scholar 

  • Hoogsteen K (1959) The structure of crystals containing a hydrogen-bonded complex of 1-methylthymine and 9-methyladenine. Acta Crystallogr 12:822–823

    Article  CAS  Google Scholar 

  • Hoogsteen K (1963) The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallogr 16:907–916

    Article  CAS  Google Scholar 

  • Hudson GA, Bloomingdale RJ, Znosko BM (2013) Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides. RNA 19:1474–1482

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huguet JM, Bizarro CV, Forns N, Smith SB, Bustamante C, Ritort F (2010) Single-molecule derivation of salt dependent base-pair free energies in DNA. Proc Natl Acad Sci U S A 107:15431–15436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huguet JM, Ribezzi-Crivellari M, Bizarro CV, Ritort F (2017) Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments. Nucleic Acids Res 45:12921–12931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iaccarino N, Cheng M, Qiu D, Pagano B, Amato J, Di Porzio A, Zhou J, Randazzo A, Mergny JL (2021) Effects of Sequence and Base Composition on the CD and TDS Profiles of i-DNA. Angew Chem Int Ed 60:10295–10303

    Article  CAS  Google Scholar 

  • Kang H-J, Kendrick S, Hecht SM, Hurley LH (2014) The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules. J Am Chem Soc 136:4172–4185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kendrick S, Akiyama Y, Hecht SM, Hurley LH (2009) The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern. J Am Chem Soc 131:17667–17676

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Knowles DB, LaCroix AS, Deines NF, Shkel I, Record Jr MT (2011) Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability. Proc Natl Acad Sci U S A 108:12699–12704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kwok CK, Ding Y, Tang Y, Assmann SM, Bevilacqua PC (2013) Determination of in vivo RNA structure in low-abundance transcripts. Nat Commun 4:2971

    Article  PubMed  Google Scholar 

  • Li XM, Zheng KW, Zhang JY, Liu HH, He YD, Yuan BF, Hao YH, Tan Z (2015) Guanine-vacancy-bearing G-quadruplexes responsive to guanine derivatives. Proc Natl Acad Sci U S A 112:14581–14586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lilley DM (2000) Structures of helical junctions in nucleic acids. Q Rev Biophys 33:109–159

    Article  CAS  PubMed  Google Scholar 

  • Lorenz R, Bernhart SH, Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P.F., and Hofacker, I.L. (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6:26

    Article  PubMed  PubMed Central  Google Scholar 

  • Lorenz R, Bernhart SH, Qin J, Honer zu Siederdissen, C., Tanzer, A., Amman, F., Hofacker, I.L., and Stadler, P.F. (2013) 2D meets 4G: G-quadruplexes in RNA secondary structure prediction. IEEE/ACM Trans Comput Biol Bioinform 10:832–844

    Article  CAS  PubMed  Google Scholar 

  • Mathad RI, Hatzakis E, Dai J, Yang D (2011) c-MYC promoter G-quadruplex formed at the 5′-end of NHE III1 element: insights into biological relevance and parallel-stranded G-quadruplex stability. Nucleic Acids Res 39:9023–9033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH (1999a) Predicting oligonucleotide affinity to nucleic acid targets. RNA 5:1458–1469

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mathews DH, Sabina J, Zuker M, Turner DH (1999b) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911–940

    Article  CAS  PubMed  Google Scholar 

  • Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A 101:7287–7292

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matsumoto S, Tateishi-Karimata H, Takahashi S, Ohyama T, Sugimoto N (2020) Effect of molecular crowding on the stability of RNA G-quadruplexes with various numbers of quartets and lengths of loops. Biochemistry

    Google Scholar 

  • Mergny JL, Lacroix L, Han XG, Leroy JL, Helene C (1995) Intramolecular folding of pyrimidine oligodeoxynucleotides into an I-DNA motif. J Am Chem Soc 117:8887–8898

    Article  CAS  Google Scholar 

  • Nagatoishi S, Isono N, Tsumoto K, Sugimoto N (2011) Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding. Biochimie 93:1231–1238

    Article  CAS  PubMed  Google Scholar 

  • Nakano S, Fujimoto M, Hara H, Sugimoto N (1999) Nucleic acid duplex stability: influence of base composition on cation effects. Nucleic Acids Res 27:2957–2965

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nakano S, Miyoshi D, Sugimoto N (2014) Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 114:2733–2758

    Article  CAS  PubMed  Google Scholar 

  • Nott TJ, Craggs TD, Baldwin AJ (2016) Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters. Nat Chem 8:569–575

    Article  CAS  PubMed  Google Scholar 

  • Ohmichi T, Nakano S, Miyoshi D, Sugimoto N (2002) Long RNA dangling end has large energetic contribution to duplex stability. J Am Chem Soc 124:10367–10372

    Article  CAS  PubMed  Google Scholar 

  • Olsen CM, Gmeiner WH, Marky LA (2006) Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking. J Phys Chem B 110:6962–6969

    Article  CAS  PubMed  Google Scholar 

  • Onel B, Carver M, Wu G, Timonina D, Kalarn S, Larriva M, Yang D (2016) A new G-quadruplex with Hairpin loop immediately upstream of the human BCL2 P1 promoter modulates transcription. J Am Chem Soc 138:2563–2570

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pandey S, Agarwala P, Maiti S (2013) Effect of loops and G-quartets on the stability of RNA G-quadruplexes. J Phys Chem B 117:6896–6905

    Article  CAS  PubMed  Google Scholar 

  • Peyret N, Seneviratne PA, Allawi HT, SantaLucia Jr J (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry 38:3468–3477

    Article  CAS  PubMed  Google Scholar 

  • Phan AT, Kuryavyi V, Burge S, Neidle S, Patel DJ (2007) Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter. J Am Chem Soc 129:4386–4392

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prakash G, Kool ET (1992) Structural effects in the recognition of DNA by circular oligonucleotides. J Am Chem Soc 114:3523–3527

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rachwal PA, Brown T, Fox KR (2007) Effect of G-tract length on the topology and stability of intramolecular DNA quadruplexes. Biochemistry 46:3036–3044

    Article  CAS  PubMed  Google Scholar 

  • Roberts RW, Crothers DM (1991) Specificity and stringency in DNA triplex formation. Proc Natl Acad Sci U S A 88:9397–9401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts RW, Crothers DM (1996) Prediction of the stability of DNA triplexes. Proc Natl Acad Sci U S A 93:4320–4325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rogers RA, Fleming AM, Burrows CJ (2018) Unusual isothermal hysteresis in DNA i-motif pH transitions: a study of the RAD17 promoter sequence. Biophys J 114:1804–1815

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS (2014) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505:701–705

    Article  CAS  PubMed  Google Scholar 

  • Ruggiero E, Lago S, Sket P, Nadai M, Frasson I, Plavec J, Richter SN (2019) A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription. Nucleic Acids Res 47:11057–11068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • SantaLucia Jr J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A 95:1460–1465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • SantaLucia J, Allawi HT, Seneviratne PA (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35:3555–3562

    Article  CAS  PubMed  Google Scholar 

  • Simonsson T, Pribylova M, Vorlickova M (2000) A nuclease hypersensitive element in the human c-myc promoter adopts several distinct i-tetraplex structures. Biochem Biophys Res Commun 278:158–166

    Article  CAS  PubMed  Google Scholar 

  • Stegle O, Payet L, Mergny JL, MacKay DJ, Leon JH (2009) Predicting and understanding the stability of G-quadruplexes. Bioinformatics 25:i374–i382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sugimoto N, Kierzek R, Turner DH (1987a) Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry 26:4554–4558

    Article  CAS  PubMed  Google Scholar 

  • Sugimoto N, Kierzek R, Turner DH (1987b) Sequence dependence for the energetics of terminal mismatches in ribooligonucleotides. Biochemistry 26:4559–4562

    Article  CAS  PubMed  Google Scholar 

  • Sugimoto N, Nakano S, Katoh M, Matsumura A, Nakamuta H, Ohmichi T, Yoneyama M, Sasaki M (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34:11211–11216

    Article  CAS  PubMed  Google Scholar 

  • Sugimoto N, Nakano S, Yoneyama M, Honda K (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24:4501–4505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sugimoto N, Nakano M, Nakano S (2000) Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes. Biochemistry 39:11270–11281

    Article  CAS  PubMed  Google Scholar 

  • Sugimoto N, Satoh N, Yasuda K, Nakano S (2001) Stabilization factors affecting duplex formation of peptide nucleic acid with DNA. Biochemistry 40:8444–8451

    Article  CAS  PubMed  Google Scholar 

  • Sun D, Hurley LH (2009) The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression. J Med Chem 52:2863–2874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takahashi S, Sugimoto N (2020) Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells. Chem Soc Rev 49:8439–8468

    Article  CAS  PubMed  Google Scholar 

  • Takahashi S, Yamamoto J, Kitamura A, Kinjo M, Sugimoto N (2019) Characterization of Intracellular Crowding Environments with Topology-Based DNA Quadruplex Sensors. Anal Chem 91:2586–2590

    Article  CAS  PubMed  Google Scholar 

  • Tinoco Jr I, Uhlenbeck OC, Levine MD (1971) Estimation of secondary structure in ribonucleic acids. Nature 230:362–367

    Article  CAS  PubMed  Google Scholar 

  • Turner DH, Mathews DH (2010) NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res 38:D280–D282

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Patel DJ (1993) Solution structure of the human telomeric repeat d [AG3 (T2AG3)3] G-tetraplex. Structure 1:263–282

    Article  CAS  PubMed  Google Scholar 

  • Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–738

    Article  CAS  PubMed  Google Scholar 

  • Wong HM, Stegle O, Rodgers S, Huppert JL (2010) A toolbox for predicting G-quadruplex formation and stability. J Nucleic Acids 2010:564946

    Article  PubMed  PubMed Central  Google Scholar 

  • Wright EP, Huppert JL, Waller ZAE (2017) Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH. Nucleic Acids Res 45:2951–2959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia T, SantaLucia Jr J, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37:14719–14735

    Article  CAS  PubMed  Google Scholar 

  • Zhang AY, Bugaut A, Balasubramanian S (2011) A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology. Biochemistry 50:7251–7258

    Article  CAS  PubMed  Google Scholar 

  • Zuker M (1989) On finding all suboptimal foldings of an RNA molecule. Science 244:48–52

    Article  CAS  PubMed  Google Scholar 

  • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133–148

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan

    Shuntaro Takahashi, Hisae Tateishi-Karimata & Naoki Sugimoto

  2. Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan

    Naoki Sugimoto

Authors
  1. Shuntaro Takahashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hisae Tateishi-Karimata
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Naoki Sugimoto
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Naoki Sugimoto .

Editor information

Editors and Affiliations

  1. Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan

    Naoki Sugimoto

Section Editor information

  1. Physical Chemistry – Biophysical Chemistry, TU Dortmund University, Dortmund, Germany

    Roland Winter

Rights and permissions

Reprints and permissions

Copyright information

© 2022 Springer Nature Singapore Pte Ltd.

About this entry

Check for updates. Verify currency and authenticity via CrossMark

Cite this entry

Takahashi, S., Tateishi-Karimata, H., Sugimoto, N. (2022). Stability Prediction of Canonical and Noncanonical Structures of Nucleic Acids. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids. Springer, Singapore. https://doi.org/10.1007/978-981-16-1313-5_2-1

Download citation

  • DOI: https://doi.org/10.1007/978-981-16-1313-5_2-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-16-1313-5

  • Online ISBN: 978-981-16-1313-5

  • eBook Packages: Springer Reference Chemistry and Mat. ScienceReference Module Physical and Materials ScienceReference Module Chemistry, Materials and Physics

Publish with us

Policies and ethics

Search

Navigation