For citation purposes: Van Dyke MW, Nelson LD. Triple helix-interacting proteins and cancer. OA Molecular Oncology 2013 Apr 01;1(1):5.

Critical review

 
Biomarkers

Triple helix-interacting proteins and cancer

MW Van Dyke1*, LD Nelson2
 

Authors affiliations

(1) Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA

(2) Department of Pediatrics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA

* Corresponding author Email: mvandyk2@kennesaw.edu

Abstract

Introduction

Although most naturally occurring DNA and RNA adopt the now quite familiar double-helix structure, certain sequences can, under appropriate conditions, adopt a three-stranded, triple-helical structure. Both intramolecular and intermolecular triplexes have been described. Evidence for the existence of triplex structures in vivo is limited, although cellular proteins have been identified that avidly and specifically interact with such species. The postulated roles of triplexes and the proteins that interact with them in cancer and their potential utility as diagnostic markers are discussed in this article.

Conclusion

More studies will be needed before the full potential of triplex nucleic acids and their role in cancer can be realised.

Introduction

Triple-helical nucleic acids

Although the right-handed double-helical structure of B-form DNA is now quite famous, having been determined in 1953 through the work of Watson and Crick among others[1,2,3], it was shortly thereafter noted that certain homopolymer DNA sequences preferentially adopted a three-stranded, triple-helical structure[4]. In this structure, the third strand lies within the major groove of the double helix, interacting with purine bases on one strand of the duplex through either Hoogsteen or reverse-Hoogsteen base pairing[5]. A schematic representation of an intermolecular triplex is shown in Figure 1A.

Triplex nucleic acids. (A) Schematic representation of an intermolecular triplex. The third strand (black) resides in the major groove of the duplex nucleic acid, hydrogen bonding to the purine-rich duplex strand. Note that the third strand may be part of a larger nucleic acid (dotted line extensions). (B) Chemical structures of T*A:T and C[+]*G:C base triplets and strand orientations present in pyrimidine motif triplexes. (C) Chemical structures of A*A:T, G*G:C, and T*A:T base triplets and strand orientations present in purine motif triplexes. An asterisk (*) indicates Hoogsteen hydrogen bonding between complementary bases; a colon (:) indicates Watson–Crick hydrogen bonding between complementary bases. Arrowhead indicates 3’ end of nucleic acid strand[48].

Two triplex motifs have been described[6,7]. In the purine motif, a purine-rich third strand binds with an antiparallel orientation relative to the complementary purine-rich acceptor strand of the duplex and the primary base triplets are G*G:C and A*A:T or T*A:T, where a colon indicates the conventional Watson–Crick base pairing present in the duplex and an asterisk reverse-Hoogsteen base pairing between bases in the third strand (G, A, or T) and purine acceptors in the target duplex. In the pyrimidine motif, a pyrimidine-rich third strand binds with a parallel orientation relative to the complementary purine-rich acceptor strand of the duplex and the primary base triplets are T*A:T and C[+]*G:C, where an asterisk indicates Hoogsteen base pairing between bases in the third strand, either thymine or protonated cytosine, and purine acceptors in the target duplex. Typical triplex DNAs range from ~10 to many tens of contiguous base triplets in length. Graphical representations of the different triplex motifs and the hydrogen bonding between nucleic acid bases are shown in Figure 1B,C.

Although most triplex structures described to date are composed exclusively of DNA, both pure RNA and mixed RNA:DNA triplex species have also been identified[8,9,10,11]. However, it should be noted that not all possible combinations of nucleic acids form stable triplexes under physiological conditions. For example, a purine motif triplex composed entirely of DNA is stable but a comparable triplex containing a single RNA strand substitution is not. Presumably this inability to form triplexes stems from structural issues regarding steric repulsion, the width of the major groove and base pitch, these factors limiting third strand accessibility to purine acceptors in the duplex. Sequence considerations are also critically important in determining the relative stability of these species, especially under physiological conditions. Thus, pyrimidine motif triplex-forming nucleic acids tend to be deficient in cytosine[12], which is not highly protonated at physiological pH given its pKa = 4.45. Similarly, purine motif triplexes are disfavoured, given the propensity for single-stranded G-rich nucleic acids to form intramolecular G-quadruplex species[13]. A listing of triplex species and their relative stability is provided in Tables 1 and 2. Note that a range of pyrimidine motif stabilities have been observed for different combinations of nucleic acids, depending on the sequence of the triplex-forming oligonucleotide being investigated. Thus, a C-rich third strand can only marginally form a pyrimidine motif D*D:D triplex, whereas a T-rich third strand forms a very stable pyrimidine motif D*D:D triplex under similar conditions.

Table 1

Purine motif triplex formation.

Table 2

Pyrimidine motif triplex formation.

Triplexes are often thought of as a separate nucleic acid molecule interacting with a target duplex. One example would be a T-rich RNA interacting with a complementary homopurine–homopyrimidine DNA duplex through intermolecular pyrimidine motif triplex formation. However, examples have been found where a homopurine–homopyrimidine DNA duplex dissociates partially into single strands (e.g. as a result of superhelical torsional strain) and one strand then forms a triplex with a proximal complementary homopurine–homopyrimidine DNA duplex present in the same molecule. These are referred to as intramolecular triplexes (Figure 2A). Both pyrimidine (H-DNA) and purine (H’-DNA) motif intramolecular triplexes have been described[14,15]. In addition, four different intramolecular triplex isomers can exist for any particular homopurine–homopyrimidine sequence, depending on which motif is involved and which half-element strand serves as the third strand (Figure 2B). Most intramolecular triplexes investigated to date have been composed entirely of DNA. However, recent studies with certain long non-coding RNAs lacking 3’ poly(A) tails (e.g. MALAT1, MENβ) have found that their intrinsic high stability results from their ability to form intramolecular pyrimidine motif RNA triplexes[16,17].

Intramolecular triplexes. (A) Schematic representation of an intramolecular triplex. The third strand (grey) resides in the major groove of the duplex nucleic acid and hydrogen bonds to the purine-rich duplex strand while its complement (white) remains primarily single-stranded. (B) Schematic representations of the four possible forms of intramolecular DNA triplexes. For H-DNA isomers H-y3 (1͇) and H-y5 (2͇), the third strand is pyrimidine-rich and originates from either the 3’ or 5’ end of an oligopyrimidine duplex strand (light grey), respectively. For H’-DNA isomers H-r3 (3͇) and H-r5 (4͇) ), the third strand is purine-rich and originates from either the 3’ or 5’ end of an oligopurine duplex strand (black), respectively[48].

Although most studies with triplexes have been performed in vitro, there is an increasing body of evidence suggesting that triplexes do exist in vivo. Immunofluorescence experiments with triplex-specific monoclonal antibodies have shown distinct staining patterns on polytene chromosomes isolated from Drosophila melanogaster[18,19]. Similarly triplex-specific antibodies exhibit multiple positive foci disseminated throughout isolated human cell nuclei[20]. Although these signals were originally thought of as evidence for intramolecular DNA*DNA:DNA triplexes, more recent studies suggest that these signals may instead reflect recognition of intermolecular RNA*DNA:DNA triplexes, which are also avidly bound by these antibodies.

Triplex-binding proteins

One line of evidence for the in vivo existence of triplex nucleic acids is the presence of endogenous proteins that specifically and avidly bind these structures. Examples of triplex-binding proteins have been found in organisms ranging from bacteria and yeast to mice and humans (Figure 3). Although the identities of several of these triplex-binding proteins are as yet unknown, for those that have been identified, many have known roles involving nucleic acids. Examples include the bacterial Tn7 protein and its role in transposon insertion[21], yeast CDP1 and chromosome segregation[22], Drosophila GAGA factor and transcriptional regulation[23], human Orc4 protein and replication[24], human XPA-RPA DNA repair complexes[25], and murine HMG proteins and a variety of DNA-dependent processes (transcription, replication, recombination and repair)[26]. Note that identified triplex-binding proteins are not limited to those that interact with DNA. Several triplex-binding proteins including the yeast ribosome-binding protein Stm1p, human pre-mRNA-binding hnRNP proteins, and human splicing factors PSF, P54nrb, U2AF65 are known RNA-binding proteins with well-established RNA-dependent biological functions in vivo[27,28,29].

Triplex-binding proteins are present in many organisms. Electrophoretic mobility shift assays were assembled containing either 0.1 nM radiolabelled purine motif triplex (A) or duplex probe (B), 2 µg poly(dI-dC) carrier DNA, and various amounts of whole cell or nuclear extracts from different organisms, as indicated. (Lane 1) control reaction, no protein. (2) 6.7 µg Escherichia coli extract. (3) 11.9 µg Dictyostelium discoideum extract. (4 & 14) 12.5 µg Saccharomyces cerevisiae extract. (5) 4.8 µg Schizosaccharomyces pombe extract. (6) 2.9 µg Drosophila melanogaster extract. (7) 15.2 µg Xenopus laevis oocyte extract. (8) 0.69 µg 3T3 mouse fibroblast nuclear extract. (9) 0.62 µg LY-apoptosis refractory mouse lymphoma nuclear extract. (10) 0.62 µg LY-apoptosis susceptible mouse lymphoma nuclear extract. (11) 0.6 µg Daudi human lymphoma nuclear extract. (12) 1.34 µg K562 human erythroleukaemia nuclear extract. (13) 4.2 µg HeLa human epithelial carcinoma nuclear extract.

Triplex structures may form in vivo. However, their presence need not always be advantageous. Intramolecular triplexes could promote undesirable recombination events or interfere with normal transcriptional controls. Thus, another aspect supporting the existence of triplex species might be the presence of proteins that destabilise these structures. RecQ-family helicases, including bacterial RecQ and human BLM and WRN, can dissociate DNA triplexes in a 3′[→]5′ direction if they initiate on a 3′ single-stranded region on the third strand[30]. In contrast, the superfamily 2 helicase FANCJ requires a 5′ single-stranded region on the third strand to dissociate triplex structures and this helicase proceeds in a 5′[→]3′ direction[31]. The absence of these proteins has been found to increase genomic instability, especially at regions having the potential to form triplex structures[32]. Finally, the nucleotide excision repair complex containing XPA can be directed to triplex structures by the associated protein RPA and thereby facilitate repair of proximal DNA photoadducts[25]. This repair, however, may only have tangential effects on triplex stability and is not the primary consequence of XPA-RPA function.

Discussion

The authors have referenced some of their own studies in this article. These referenced studies have been conducted in accordance with the Declaration of Helsinki (1964) and the protocols of these studies have been approved by the relevant ethics committees related to the institution in which they were performed. All human subjects in these studies gave their informed consent for their participation and use of derived materials.

Triple-helical nucleic acids and cancer

Although the existence of persistent triple-helical structures in vivo is as yet not fully endorsed by the scientific community, several lines of evidence implicating triplexes in cancer have been described. Sequences capable of forming H-DNA are abundant in mammalian genomes and these sequences often correspond to sites of increased susceptibility to chromosomal translocations (e.g. the promoter region of the c-MYC oncogene and c-MYC translocations present in several lymphomas and leukaemias)[33,34]. Both intermolecular and intramolecular DNA triplexes have been shown to be mutagenic, promoting both recombination and DNA repair. More recently, the unexpected stability of certain long non-coding RNAs involved in cancer, including Kaposi’s sarcoma-associated herpes virus polyadenylated nuclear (PAN), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), and multiple endocrine neoplasia-β (MENβ) RNAs have been found to be the result of intramolecular RNA triplex formation near their 3′ ends[16,17,35].

Triplex-dissociating helicases and cancer

If triplexes exist and promote cancer, then the loss of proteins that prevent triplex formation and/or dissociate triplex structures should promote cancer. This is true for the DNA helicases BLM and WRN and for the bifunctional RNA and DNA helicase FANCJ. BLM is part of the BRCA1-associated genome surveillance complex and is normally involved in DNA replication and repair[36]. Defects in BLM are the cause of Bloom’s syndrome, characterised by proportionate prenatal and postnatal growth deficiency, sun-sensitive telangiectatic hypopigmented and hyperpigmented skin, predisposition to general malignancy and chromosomal instability[37]. WRN has both helicase and exonuclease activities and is involved in resolving inappropriate structures during recombination, DNA replication and repair[38]. Defects in WRN are the cause of Werner syndrome, characterised by the premature onset of multiple age-related disorders, including atherosclerosis, non-insulin-dependent diabetes mellitus, ocular cataracts, osteoporosis and the appearance of rare cancers (e.g. osteosarcomas and chondrosarcomas)[39]. FANCJ (also known as BRIP1 or BACH1) is also associated with BRCA1 and is normally involved in DNA double-strand break repair by homologous recombination[40]. Defects in FANCJ are the cause of Fanconi anaemia complementation group J and result in anaemia, leukopaenia and thrombopaenia. Loss of FANCJ has been described in several cancers but especially associated with breast carcinomas. However, it should be noted that while all of these helicases can act upon triplex structures, they can also act upon other non-B structures (e.g. G-quadruplex, cruciform, slipped-strands) as well as normal duplex nucleic acids[42]. Thus, it cannot be said for certain which structure’s resolution is most responsible for the effects of these helicases on cancer.

Triplex-binding proteins and cancer

With like reasoning, if triplexes exist and promote cancer, then proteins that facilitate triplex formation and/or stabilise triplex structures may promote cancer. This has been more difficult to establish for triplex-binding proteins. For example, while the human Orc4 protein plays an essential role in the initiation of replication and has been found to preferentially bind pyrimidine motif triplex DNA, overexpression of this protein has not been strongly implicated in any cancer[24,43]. Certain high mobility group proteins (e.g. HMGB1) have been reported to promote the formation of purine motif triplexes[26]. However, they are well known to interact with other nucleic acid structures, preferentially single-stranded DNA, and have paradoxical oncogenic and tumour suppressive roles in several cancers[44,45]. Finally, while RPA preferentially directs XPA to DNA damage proximal to triplexes and facilitates repair, overexpression of RPA adversely impacts homologous recombination and elevated genomic instability, suggesting that the aforementioned repair does not reduce the incidence of certain cancers[46].

The best evidence for a relationship between triplex-binding proteins and cancer can be found in the recent work of Nelson et al.[29] Examining extracts from 63 human colorectal tumour and adjacent normal tissues using an electrophoretic mobility shift assay (EMSA), they found significantly higher levels of one triplex species (H3, originally described by Musso et al.[47]) in tumour extracts than in corresponding normal tissue extracts. The ratio of H3 observed in tumour versus normal tissue (T/N) significantly correlated with lymph node disease (N-stage), metastasis and a reduction in overall survival following 65 months observation. However, similar correlations were not observed for other triplex species observed in these extracts. Using affinity chromatography, nano-scale high-performance liquid chromatography and electrospray ionisation tandem mass spectrometry, they were able to identify three proteins specifically bound to their purine motif triplex DNA probe: 100-kDa polypyrimidine-tract binding-associated splicing factor PSF, 60-kDa nuclear RNA-binding protein P54nrb, and 65-kDa U2 small nuclear RNA auxiliary factor 2 isoform b. PSF and P54nrb form heterodimers and function as RNA polymerase II-associated splicing factors. U2AF65 is also a known RNA polymerase II-associated splicing factor, involved in the recognition of degenerate pyrimidine tracts downstream of the branch point during spliceosome assembly. Involvement of U2AF65 in the H3 species was confirmed using anti-U2AF65 MC3 antibody and a super-shift EMSA experiment. The roles of PSF or P54nrb in any other EMSA species were not confirmed. Of the 63 patient samples 51 were then investigated by western blotting. This confirmed U265AF correlation with H3 levels and showed increased expression in advanced clinical stages (UICC Stage III and IV, Dukes C and D). Similar correlations could not be made with either PSF or P54nrb. Curiously, western blotting indicated a strong correlation between H3 levels and the DNA helicase WRN, suggesting coordinate regulation of triplex-stabilising and triplex-destabilising activities.

Conclusion

Are triplexes and/or their interacting proteins suitable markers for cancer prognosis, diagnosis or targeting? This remains an open question at this time. Multiple lines of evidence suggesting the existence of triplex nucleic acids in vivo do exist. However, they are far from conclusive. Fundamental knowledge as to the exact types of triplex present: DNA, RNA or hybrid, pyrimidine motif or purine motif, intramolecular or intermolecular, as yet remains unanswered. Once a better understanding of triplex physiology has been achieved, then studies such as those of Nelson et al. can be undertaken to directly assess the role of these structures in tumour progression for different cancers. Note that further studies of triplex-interacting proteins, both stabilising and destabilising, are still potentially worthwhile. However, regardless of the observed strength of correlations found, studies with these proteins cannot be considered conclusive proof for a role of triplexes in cancer. To date for the limited number of triplex-interacting proteins identified, all have additional described biological roles beyond those involving triplex structures. For example, triplex-disrupting helicases including BLM, WRN and FANCJ can act upon other non-B form structures, including cruciforms, D-loops, G-quadruplexes, and slipped strands. Similarly, the described triplex-binding proteins are also known to avidly bind a variety of nucleic acid structures, ranging from single strands to branched nucleic acids. Thus, the identification of proteins that specifically and exclusively recognise triplex structures is paramount. In conclusion, more studies will be needed before the full potential of triplex nucleic acids and their role in cancer can be realised.

Acknowledgements

MW Van Dyke is supported by the National Institute of General Medical Sciences (1R15GM104833-01) and was supported by a Faculty Research and Creative Activities Award from his previous institution (Western Carolina University, Cullowhee NC, USA).

Authors Contribution

All authors contributed to the conception, design, and preparation of the manuscript, as well as read and approved the final manuscript.

Competing interests

None declared.

Conflict of Interests

None declared.

A.M.E

All authors abide by the Association for Medical Ethics (AME) ethical rules of disclosure.

References

  • 1. Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 1953 Apr;171(4356):737-8.
  • 2. Wilkins MH, Stokes AR, Wilson HR. Molecular structure of deoxypentose nucleic acids. Nature 1953 Apr;171(4356):738-40.
  • 3. Franklin RE, Gosling RG. Molecular configuration in sodium thymonucleate. Nature 1953 Apr;171(4356):740-1.
  • 4. Felsenfeld G, Davies DR, Rich A. Formation of a three-stranded polynucleotide molecule. J Am Chem Soc 1957 Apr;79(8):2023-4.
  • 5. Hoogsteen K . The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Cryst 1963 Sep;16(9):907-16.
  • 6. Mirkin SM, Frank-Kamenetskii MD. H-DNA and related structures. Annu Rev Biophys Biomol Struct 1994;23541-76.
  • 7. Frank-Kamenetskii MD, Mirkin SM. Triplex DNA structures. Annu Rev Biochem 1995;6465-95.
  • 8. Roberts RW, Crothers DM. Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science 1992 Nov;258(5087):1463-6.
  • 9. Han H, Dervan PB. Sequence-specific recognition of double helical RNA and RNA. DNA by triple helix formation. Proc Natl Acad Sci USA 1993 May;90(9):3806-10.
  • 10. Escudé C, François JC, Sun JS, Ott G, Sprinzl M, Garestier T. Nucleic Acids Res 1993 Dec;21(24):5547-53.
  • 11. Semerad CL, Maher LJ. Exclusion of RNA strands from a purine motif triple helix. Nucleic Acids Res 1994 Dec;22(24):5321-5.
  • 12. Morgan AR, Wells RD. Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J Mol Biol 1968 Oct;37(1):63-80.
  • 13. Cheng AJ, Van Dyke MW. Monovalent cation effects on intermolecular purine–purine–pyrimidine triple-helix formation. Nucleic Acids Res 1993 Dec;21(24):5630-5.
  • 14. Htun H, Dahlberg JE. Topology and formation of triple-stranded H-DNA. Science 1989 Mar;243(4898):1571-6.
  • 15. Kohwi Y, Kohwi-Shigematsu T. Magnesium ion-dependent triple-helix structure formed by homoprine–homopyrimidine sequences in supercoiled plasmid DNA. Proc Natl Acad Sci USA 1988 Jun;85(11):3781-5.
  • 16. Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA. A triple helix stabilizes the 3’ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 2012 Nov;26(21):2392-407.
  • 17. Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA. Formation of triple-helical structures by the 3’-end sequences of MALAT1 and MENβ noncoding RNAs. Proc Natl Acad Sci USA 2012 Nov;109(47):19202-7.
  • 18. Burkholder GD, Latimer LJ, Lee JS. Immunofluorescent localization of triplex DNA in polytene chromosomes of Chironomus and Drosophila. Chromosoma 1991 Oct;101(1):11-8.
  • 19. Gorab E, Amabis JM, Stocker AJ, Drummond L, Stollar BD. Potential sites of triple-helical nucleic acid formation in chromosomes of Rhynchosciara (Diptera: Sciaridae) and Drosophila melanogaster. Chromosome Res 2009;17(6):821-32.
  • 20. Ohno M, Fukagawa T, Lee JS, Ikemura T. Triplex-forming DNAs in the human interphase nucleus visualized in situ by polypurine/polypyrimidine DNA probes and antitriplex antibodies. Chromosoma 2002 Sep;111(3):201-13.
  • 21. Rao JE, Craig NL. Selective recognition of pyrimidine motif triplexes by a protein encoded by the bacterial transposon Tn7. J Mol Biol 2001 Apr;307(5):1161-70.
  • 22. Musso M, Bianchi-Scarr G, Van Dyke MW. The yeast CDP1 gene encodes a triple-helical DNA-binding protein. Nucleic Acids Res 2000 Nov;28(21):4090-6.
  • 23. Jiménez-García E, Vaquero A, Espinás ML, Soliva R, Orozco M, Bernués J. The GAGA factor of Drosophila binds triple-stranded DNA. J Biol Chem 1998 Sep;273(38):24640-8.
  • 24. Kusic J, Tomic B, Divac A, Kojic S. Human initiation protein Orc4 prefers triple stranded DNA. Mol Biol Rep 2010 Jun;37(5):2317-22.
  • 25. Thoma BS, Wakasugi M, Christensen J, Reddy MC, Vasquez KM. Human XPC-hHR23B interacts with XPA-RPA in the recognition of triplex-directed psoralen DNA interstrand crosslinks. Nucleic Acids Res 2005 May;33(9):2993-3001.
  • 26. Suda T, Mishima Y, Takayanagi K, Asakura H, Odani S, Kominami R. A novel activity of HMG domains: promotion of the triple-stranded complex formation between DNA containing (GGA/TCC)11 and d(GGA)11 oligonucleotides. Nucleic Acids Res 1996 Dec;24(23):4733-40.
  • 27. Nelson LD, Musso M, Van Dyke MW. The yeast STM1 gene encodes a purine motif triple helical DNA-binding protein. J Biol Chem 2000 Feb;275(8):5573-81.
  • 28. Guillonneau F, Guieysse AL, Le Caer JP, Rossier J, Praseuth D. Selection and amplification of proteins bound to DNA triple-helical structures by combination of 2D-electrophoresis and MALDI-TOF mass spectrometry. Nucleic Acids Res 2001 Jun;29(11):2427-36.
  • 29. Nelson LD, Bender C, Mannsperger H, Buergy D, Kambakamba P, Mudduluru G. Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer. Mol Cancer 2012 Jun;1138.
  • 30. Brosh RM, Majumdar A, Desai S, Hickson ID, Bohr VA, Seidman MM. Unwinding of a DNA triple helix by the Werner and Bloom syndrome helicases. J Biol Chem 2001 Feb;276(5):3024-30.
  • 31. Sommers JA, Rawtani N, Gupta R, Bugreev DV, Mazin AV, Cantor SB. FANCJ uses its motor ATPase to destabilize protein-DNA complexes, unwind triplexes, and inhibit RAD51 strand exchange. J Biol Chem 2009 Mar;284(12):7505-17.
  • 32. Chu WK, Hickson ID. RecQ helicases: multifunctional genome caretakers. Nat Rev Cancer 2009 Sep;9(9):644-54.
  • 33. Joos S, Haluska FG, Falk MH, Henglein B, Hameister H, Croce CM. Mapping chromosomal breakpoints of Burkitt’st(8;14) translocations far upstream of c-myc. Cancer Res 1992 Dec;52(23):6547-52.
  • 34. Wang G, Vasquez KM. Naturally occurring H-DNA-forming sequences are mutagenic in mammalian cells. Proc Natl Acad Sci USA 2004 Sep;101(37):13448-53.
  • 35. Mitton-Fry RM, DeGregorio SJ, Wang J, Steitz TA, Steitz JA. Poly(A) tail recognition by a viral RNA element through assembly of a triple helix. Science 2010 Nov;330(6008):1244-7.
  • 36. Wang Y, Cortez D, Yazdi P, Neff N, Elledge SJ, Qin J. BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. Genes Dev 2000 Apr 15;14(8):927-39.
  • 37. German J, Sanz MM, Ciocci S, Ye TZ, Ellis NA. Syndrome-causing mutations of the BLM gene in persons in the Bloom’s Syndrome Registry. Hum Mutat 2007 Aug;28(8):743-53.
  • 38. Sidorova JM . Roles of the Werner syndrome RecQ helicase in DNA replication. DNA Repair (Amst) 2008 Nov;7(11):1776-86.
  • 39. Ishikawa Y, Miller RW, Machinami R, Sugano H, Goto M. A typical osteosarcomas in Werner Syndrome (adult progeria). Jpn J Cancer Res 2000 Dec;91(12):1345-9.
  • 40. Cantor SB, Bell DW, Ganesan S, Kass EM, Drapkin R, Grossman S. BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function. Cell 2001 Apr;105(1):149-60.
  • 41. Cantor SB, Guillemette S. Hereditary breast cancer and the BRCA1-associated FANCJ/BACH1/BRIP1. Future Oncol 2011 Feb;7(2):253-61.
  • 42. Sharma S . Non-B DNA secondary structures and their resolution by RecQ helicases. J Nucleic Acids 2011724215.
  • 43. Radojkovic M, Ristic S, Divac A, Tomic B, Nestorovic A, Radojkovic D. Novel ORC4L gene mutation in B-cell lymphoproliferative disorders. Am J Med Sci 2009 Dec;338(6):527-9.
  • 44. Stros M . HMGB proteins: interactions with DNA and chromatin. Biochim Biophys Acta 2010 Jan–Feb;1799(1–2):101-13.
  • 45. Kang R, Zhang Q, Zeh HJ, Lotze MT, Tang D. HMGB1 in cancer: good, bad, or both?. Clin Cancer Res 2013 Aug;19(15):4046-57.
  • 46. Outwin E, Carpenter G, Bi W, Withers MA, Lupski JR, O’Driscoll M. Increased RPA1 gene dosage affects genomic stability potentially contributing to 17p13.3 duplication syndrome. PLoS Genet 2011 Aug;7(8):e1002247.
  • 47. Musso M, Nelson LD, Van Dyke MW. Characterization of purine motif triplex DNA-binding proteins in HeLa extracts. Biochemistry 1998 Mar;37(9):3086-95.
  • 48. Van Dyke MW . Do DNA triple helices or quadruplexes have a role in transcription? In: DNA conformation and transcription. Landes Bioscience 2005p105-26.
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Purine motif triplex formation.

Triplex → Strand↓ D*D:D D*D:R D*R:D D*R:R R*D:D R*D:R R*R:D R*R:R
3 D D D D R R R R
Pu D D R R D D R R
Py D R D R D R D R
Stability +++ ~ ~

Pyrimidine motif triplex formation.

Triplex →Strand↓ D*D:D D*D:R D*R:D D*R:R R*D:D R*D:R R*R:D R*R:R
3 D D D D R R R R
Pu D D R R D D R R
Py D R D R D R D R
Stability ~/+++ ~/++ +++/++ ++/+++ ~/+ +/~

(D) DNA, (R) RNA, (*) Hoogsteen or reverse-Hoogsteen hydrogen bonding, (:) Watson-Crick hydrogen bonding, (3) third strand of triplex, (Pu) purine-rich strand of duplex, (Py) pyrimidine-rich strand of duplex. Relative triplex stabilities range from none (–), marginal (~), weak (+), moderate (++) to strong (+++). Multiple stabilities indicate values observed for different triplex sequences. First value is dominant among three independent investigations8,9,10.