View source for Helicase

{{short description|Class of enzymes that unpack genetic material}}
[[Image:Helicase.png|thumb|upright=1.2|Structure of ''[[Escherichia coli|E. coli]]'' helicase RuvA (note that the heilcase core in RuvAB complex is RuvB and not RuvA and that RuvA alone do not show helicase activity)]]
'''Helicases''' are a class of [[enzyme]]s that are vital to all [[organism]]s. Their main function is to unpack an organism's [[DNA|genetic material]]. Helicases are [[motor protein]]s that move [[Directionality (molecular biology)|directionally]] along a [[Nucleic acid double helix|nucleic double helix]], separating the two hybridized nucleic acid strands (hence ''[[nucleic acid double helix|helic-]] + [[wikt:-ase#Suffix|-ase]]''), via the energy gained from [[adenosine triphosphate|ATP]] [[hydrolysis]]. There are many helicases, representing the great variety of processes in which strand separation must be catalyzed. Approximately 1% of eukaryotic genes code for helicases.<ref name="wu">{{cite journal | vauthors = Wu Y | title = Unwinding and rewinding: double faces of helicase? | journal = Journal of Nucleic Acids | volume = 2012 | pages = 140601 | year = 2012 | pmid = 22888405 | pmc = 3409536 | doi = 10.1155/2012/140601 | doi-access = free }}</ref>

The [[human genome]] codes for 95 non-redundant helicases: 64 RNA helicases and 31 DNA helicases.<ref name="Umate">{{cite journal | vauthors = Umate P, Tuteja N, Tuteja R | title = Genome-wide comprehensive analysis of human helicases | journal = Communicative & Integrative Biology | volume = 4 | issue = 1 | pages = 118–137 | date = January 2011 | pmid = 21509200 | pmc = 3073292 | doi = 10.4161/cib.13844 }}</ref> Many cellular processes, such as [[DNA replication]], [[transcription (genetics)|transcription]], [[translation (biology)|translation]], [[genetic recombination|recombination]], [[DNA repair]] and [[ribosome biogenesis]] involve the separation of nucleic acid strands that necessitates the use of helicases. Some specialized helicases are also involved in sensing viral nucleic acids during infection and fulfill an immunological function. [[Genetic mutations]] that affect helicases can have wide-reaching impacts for an organism, due to their [[Conserved sequence#Mechanisms|significance in many biological processes]].

== Function ==

Helicases are often used to separate strands of a [[DNA]] [[double helix]] or a self-annealed [[RNA]] molecule using the energy from [[adenosine triphosphate|ATP]] hydrolysis, a process characterized by the breaking of [[hydrogen bond]]s between [[base pair|annealed nucleotide bases]]. They also function to remove nucleic acid-associated proteins and catalyze homologous [[genetic recombination|DNA recombination]].<ref name="Patel2006">{{cite journal | vauthors = Patel SS, Donmez I | title = Mechanisms of helicases | journal = The Journal of Biological Chemistry | volume = 281 | issue = 27 | pages = 18265–18268 | date = July 2006 | pmid = 16670085 | doi = 10.1074/jbc.R600008200 | doi-access = free }}</ref> Metabolic processes of RNA such as translation, transcription, [[ribosome biogenesis]], [[RNA splicing]], RNA transport, [[RNA editing]], and RNA degradation are all facilitated by helicases.<ref name=Patel2006 /> Helicases move incrementally along one [[nucleic acid]] strand of the duplex with a [[directionality (molecular biology)|directionality]] and [[processivity]] specific to each particular enzyme.

Helicases adopt different structures and [[oligomerization]] states. Whereas [[dnaB helicase|DnaB]]-like helicases unwind [[DNA]] as ring-shaped [[hexamer]]s, other enzymes have been shown to be active as [[monomer]]s or [[protein dimer|dimer]]s. Studies have shown that helicases may act passively, waiting for uncatalyzed unwinding to take place and then translocating between displaced strands,<ref name=Croquette>{{cite journal | vauthors = Lionnet T, Spiering MM, Benkovic SJ, Bensimon D, Croquette V | title = Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 50 | pages = 19790–19795 | date = December 2007 | pmid = 18077411 | pmc = 2148377 | doi = 10.1073/pnas.0709793104 | doi-access = free | bibcode = 2007PNAS..10419790L }}</ref> or can play an active role in catalyzing strand separation using the energy generated in ATP hydrolysis.<ref name="Johnson_2007">{{cite journal | vauthors = Johnson DS, Bai L, Smith BY, Patel SS, Wang MD | title = Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase | journal = Cell | volume = 129 | issue = 7 | pages = 1299–1309 | date = June 2007 | pmid = 17604719 | pmc = 2699903 | doi = 10.1016/j.cell.2007.04.038 }}</ref> In the latter case, the helicase acts comparably to an active motor, unwinding and translocating along its substrate as a direct result of its ATPase activity.<ref name=physorg1>{{cite web |url=http://www.physorg.com/news102663442.html |title=Researchers solve mystery of how DNA strands separate |date=2007-07-03 |access-date=2007-07-05}}</ref> Helicases may process much faster ''[[in vivo]]'' than ''[[in vitro]]'' due to the presence of accessory proteins that aid in the destabilization of the fork junction.<ref name=physorg1 />

{{Plain image with caption|DNA_replication en.svg|Helicase (blue triangle) separates the intertwined DNA strands so that [[DNA replication|daughter strands can form]]. |650px|center|bottom|triangle|darkblue}}

=== Activation barrier in helicase activity ===
Enzymatic helicase action, such as unwinding nucleic acids, is achieved through the lowering of the activation barrier (<math>B</math>) of each specific action.<ref name="Betterton_2005">{{Cite journal | vauthors = Betterton MD, Jülicher F |date=2005-08-31 |title=Erratum: Opening of nucleic-acid double strands by helicases: Active versus passive opening [Phys. Rev. E 71, 011904 (2005)] |url=https://link.aps.org/doi/10.1103/PhysRevE.72.029906 |journal=Physical Review E |volume=72 |issue=2 |pages=029906 |doi=10.1103/PhysRevE.72.029906|bibcode=2005PhRvE..72b9906B }}</ref><ref name="Johnson_2007"/><ref name="manosas">{{cite journal | vauthors = Manosas M, Xi XG, Bensimon D, Croquette V | title = Active and passive mechanisms of helicases | journal = Nucleic Acids Research | volume = 38 | issue = 16 | pages = 5518–5526 | date = September 2010 | pmid = 20423906 | pmc = 2938219 | doi = 10.1093/nar/gkq273 }}</ref><ref name="Jarillo_2021">{{cite journal | vauthors = Jarillo J, Ibarra B, Cao-García FJ | title = DNA replication: ''In vitro'' single-molecule manipulation data analysis and models | journal = Computational and Structural Biotechnology Journal | volume = 19 | pages = 3765–3778 | date = 2021 | pmid = 34285777 | pmc = 8267548 | doi = 10.1016/j.csbj.2021.06.032 }}</ref> The activation barrier is a result of various factors, and can be defined by
: <math>B=N(\Delta G_\text{bp}-G_\text{int}-G_\text{f})</math>
where
* <math>N</math> = number of unwound base pairs (bps),
* <math>\Delta G_\text{bp}</math> = free energy of base pair formation,
* <math>G_\text{int}</math> = reduction of free energy due to helicase, and
* <math>G_\text{f}</math> = reduction of free energy due to unzipping forces.
Factors that contribute to the height of the activation barrier include: specific nucleic acid sequence of the molecule involved, the number of base pairs involved, tension present on the replication fork, and destabilization forces.<ref name="Betterton_2005" /><ref name="Johnson_2007" /><ref name="manosas" /><ref name="Jarillo_2021" />

=== Active and passive helicases ===
The size of the activation barrier to overcome by the helicase contributes to its classification as an active or passive helicase. In passive helicases, a significant activation barrier exists (defined as <math>B> k_\text{B}T</math>, where <math>k_\text{B}</math> is the [[Boltzmann constant]] and <math>T</math> is temperature of the system). Due to this significant activation barrier, its unwinding progression is affected largely by the sequence of nucleic acids within the molecule to unwind, and the presence of destabilization forces acting on the replication fork.<ref name="Betterton_2005" /><ref name="Johnson_2007" /><ref name="manosas" /><ref name="Jarillo_2021" /> Certain nucleic acid combinations will decrease unwinding rates (i.e. [[guanine]] and [[cytosine]]), while various destabilizing forces can increase the unwinding rate.<ref name="Johnson_2007" /><ref name="manosas" /><ref name="Jarillo_2021" /> In passive systems, the rate of unwinding (<math>V_{un}</math>) is less than the rate of translocation (<math>V_{trans}</math>) (translocation along the single-strand nucleic acid, ssNA), due to its reliance on the transient unraveling of the base pairs at the replication fork to determine its rate of unwinding.<ref name="Betterton_2005" /><ref name="Johnson_2007" /><ref name="manosas" /><ref name="Jarillo_2021" />

In active helicases, <math>B< k_\text{B}T</math>, where the system lacks a significant barrier, as the helicase can destabilize the nucleic acids, unwinding the double-helix at a constant rate, regardless of the nucleic acid sequence. In active helicases, <math>V_\text{un}</math> is closer to <math>V_\text{trans}</math>, due to the active helicase ability to directly destabilize the replication fork to promote unwinding.<ref name="Betterton_2005" /><ref name="Johnson_2007" /><ref name="manosas" /><ref name="Jarillo_2021" />

Active helicases show similar behaviour when acting on both double-strand nucleic acids, dsNA, or ssNA, in regards to the rates of unwinding and rates of translocation, where in both systems <math>V_\text{un}</math> and <math>V_\text{trans}</math> are approximately equal.

These two categories of helicases may also be modeled as mechanisms. In such models, the passive helicases are conceptualized as Brownian ratchets, driven by thermal fluctuations and subsequent anisotropic gradients across the DNA lattice. The active helicases, in contrast, are conceptualized as stepping motors – also known as powerstroke motors – utilizing either a conformational "inch worm" or a hand-over-hand "walking" mechanism to progress.<ref>Wu, C. G. and Spies, M.: Overview: What are Helicases? In: Spies, M. (Ed.): [https://www.worldcat.org/oclc/821265762]. Springer Science+Business Media, NY, 2013</ref> Depending upon the organism, such helix-traversing progress can occur at rotational speeds in the range of 5,000 <ref>{{cite web |title=Kevin Ahern's Biochemistry (BB 451/551) at Oregon State University |url=http://oregonstate.edu/instruct/bb451/winter13/lectures/highlightsdnareplic1.html |archive-url=https://web.archive.org/web/20210126121654/http://oregonstate.edu/instruct/bb451/winter13/lectures/highlightsdnareplic1.html |archive-date=2021-01-26 |access-date=2024-01-03 |website=oregonstate.edu}}</ref> to 10,000 <ref>3-D Animation Library; Replication: [https://www.dnalc.org/resources/3d/04-mechanism-of-replication-advanced.html] (Advanced)</ref>  R.P.M.

== History of DNA helicases ==
DNA helicases were discovered in ''E. coli'' in 1976. This helicase was described as a "DNA unwinding enzyme" that is "found to denature DNA duplexes in an ATP-dependent reaction, without detectably degrading".<ref name="Abdel">{{cite journal | vauthors = Abdel-Monem M, Dürwald H, Hoffmann-Berling H | title = Enzymic unwinding of DNA. 2. Chain separation by an ATP-dependent DNA unwinding enzyme | journal = European Journal of Biochemistry | volume = 65 | issue = 2 | pages = 441–449 | date = June 1976 | pmid = 133023 | doi = 10.1111/j.1432-1033.1976.tb10359.x | doi-access = free }}</ref> The first eukaryotic DNA helicase discovered was in 1978 in the lily plant.<ref name="Hotta">{{cite journal | vauthors = Hotta Y, Stern H | title = DNA unwinding protein from meiotic cells of Lilium | journal = Biochemistry | volume = 17 | issue = 10 | pages = 1872–1880 | date = May 1978 | pmid = 207302 | doi = 10.1021/bi00603a011 }}</ref> Since then, DNA helicases were discovered and isolated in other bacteria, viruses, yeast, flies, and higher eukaryotes.<ref name="Venkatesan_1982">{{cite journal | vauthors = Venkatesan M, Silver LL, Nossal NG | title = Bacteriophage T4 gene 41 protein, required for the synthesis of RNA primers, is also a DNA helicase | journal = The Journal of Biological Chemistry | volume = 257 | issue = 20 | pages = 12426–12434 | date = October 1982 | pmid = 6288720 | doi = 10.1016/S0021-9258(18)33731-1 | doi-access = free }}</ref> To date, at least 14 different helicases have been isolated from single celled organisms, 6 helicases from bacteriophages, 12 from viruses, 15 from yeast, 8 from plants, 11 from calf thymus, and approximately 25 helicases from human cells.<ref name="pmid15128294"/> Below is a history of helicase discovery:
* '''1976''' – Discovery and isolation of ''E. coli''-based DNA helicase<ref name="Abdel"/>
* '''1978''' – Discovery of the first eukaryotic DNA helicases, isolated from the lily plant<ref name="Hotta"/>
* '''1982''' – "T4 gene 41 protein" is the first reported bacteriophage DNA helicase<ref name="Venkatesan_1982"/>
* '''1985''' – First mammalian DNA helicases isolated from calf thymus<ref>{{cite journal | vauthors = Hübscher U, Stalder HP | title = Mammalian DNA helicase | journal = Nucleic Acids Research | volume = 13 | issue = 15 | pages = 5471–5483 | date = August 1985 | pmid = 3162158 | pmc = 321884 | doi = 10.1093/nar/13.15.5471 }}</ref>
* '''1986''' – SV40 large tumor antigen reported as a viral helicase (1st reported viral protein that was determined to serve as a DNA helicase)<ref name="pmid3019672">{{cite journal | vauthors = Stahl H, Dröge P, Knippers R | title = DNA helicase activity of SV40 large tumor antigen | journal = The EMBO Journal | volume = 5 | issue = 8 | pages = 1939–1944 | date = August 1986 | pmid = 3019672 | pmc = 1167061 | doi = 10.1002/j.1460-2075.1986.tb04447.x }}</ref>
* '''1986''' – ATPaseIII, a yeast protein, determined to be a DNA helicase<ref name="pmid3017945">{{cite journal | vauthors = Sugino A, Ryu BH, Sugino T, Naumovski L, Friedberg EC | title = A new DNA-dependent ATPase which stimulates yeast DNA polymerase I and has DNA-unwinding activity | journal = The Journal of Biological Chemistry | volume = 261 | issue = 25 | pages = 11744–11750 | date = September 1986 | pmid = 3017945 | doi = 10.1016/S0021-9258(18)67306-5 | doi-access = free }}</ref>
* '''1988''' – Discovery of seven conserved amino acid domains determined to be helicase motifs
* '''1989''' – Designation of DNA helicase Superfamily I and Superfamily II<ref name="pmid2546125">{{cite journal | vauthors = Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM | title = Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes | journal = Nucleic Acids Research | volume = 17 | issue = 12 | pages = 4713–4730 | date = June 1989 | pmid = 2546125 | pmc = 318027 | doi = 10.1093/nar/17.12.4713 }}</ref>
* '''1989''' – Identification of the DEAD box helicase family<ref>Linder, P., Lasko, P.F., Ashburner, M., Leroy, P., Nielson, P.J., Nishi, K., Schneir, J., Slonimski, P.P. (1989) Birth of the DEAD-box. Nature (London) 337, 121-122.</ref>
* '''1990''' – Isolation of a human DNA helicase<ref name="pmid1702201">{{cite journal | vauthors = Tuteja N, Tuteja R, Rahman K, Kang LY, Falaschi A | title = A DNA helicase from human cells | journal = Nucleic Acids Research | volume = 18 | issue = 23 | pages = 6785–6792 | date = December 1990 | pmid = 1702201 | pmc = 332732 | doi = 10.1093/nar/18.23.6785 }}</ref>
* '''1992''' – Isolation of the first reported mitochondrial DNA helicase (from bovine brain)<ref name="pmid1326759">{{cite journal | vauthors = Hehman GL, Hauswirth WW | title = DNA helicase from mammalian mitochondria | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 89 | issue = 18 | pages = 8562–8566 | date = September 1992 | pmid = 1326759 | pmc = 49960 | doi = 10.1073/pnas.89.18.8562 | doi-access = free | bibcode = 1992PNAS...89.8562H }}</ref>
* '''1996''' – Report of the discovery of the first purified chloroplast DNA helicase from the pea<ref name="pmid8665952">{{cite journal | vauthors = Tuteja N, Phan TN, Tewari KK | title = Purification and characterization of a DNA helicase from pea chloroplast that translocates in the 3'-to-5' direction | journal = European Journal of Biochemistry | volume = 238 | issue = 1 | pages = 54–63 | date = May 1996 | pmid = 8665952 | doi = 10.1111/j.1432-1033.1996.0054q.x | doi-access = free }}</ref>
* '''2002''' – Isolation and characterization of the first biochemically active malarial parasite DNA helicase – ''Plasmodium cynomolgi''.<ref name="pmid12387853">{{cite journal | vauthors = Tuteja R, Malhotra P, Song P, Tuteja N, Chauhan VS | title = Isolation and characterization of an eIF-4A homologue from Plasmodium cynomolgi | journal = Molecular and Biochemical Parasitology | volume = 124 | issue = 1–2 | pages = 79–83 | year = 2002 | pmid = 12387853 | doi = 10.1016/S0166-6851(02)00205-0 }}</ref>

== Structural features ==
The common function of helicases accounts for the fact that they display a certain degree of [[amino acid]] [[sequence homology]]; they all possess [[sequence motif]]s located in the interior of their [[primary structure]], involved in [[adenosine triphosphate|ATP]] binding, ATP [[hydrolysis]] and translocation along the [[nucleic acid]] [[substrate (biochemistry)|substrate]]. The variable portion of the [[amino acid]] sequence is related to the specific features of each helicase.

The presence of these helicase motifs allows putative helicase activity to be attributed to a given protein, but does not necessarily confirm it as an active helicase. [[Conserved sequence|Conserved motifs]] do, however, support an evolutionary homology among enzymes. Based on these helicase motifs,  a number of helicase superfamilies have been distinguished.

== Superfamilies ==
Helicases are classified in 6 groups (superfamilies) based on their shared sequence motifs.<ref name="singleton">{{cite journal | vauthors = Singleton MR, Dillingham MS, Wigley DB | title = Structure and mechanism of helicases and nucleic acid translocases | journal = Annual Review of Biochemistry | volume = 76 | pages = 23–50 | year = 2007 | pmid = 17506634 | doi = 10.1146/annurev.biochem.76.052305.115300 }}</ref> Helicases not forming a ring structure are in superfamilies 1 and 2, and ring-forming helicases form part of superfamilies 3 to 6.<ref name="Fairman">{{cite journal | vauthors = Fairman-Williams ME, Guenther UP, Jankowsky E | title = SF1 and SF2 helicases: family matters | journal = Current Opinion in Structural Biology | volume = 20 | issue = 3 | pages = 313–324 | date = June 2010 | pmid = 20456941 | pmc = 2916977 | doi = 10.1016/j.sbi.2010.03.011 }}</ref> Helicases are also classified as α or β depending on if they work with single or double-strand [[DNA]]; α helicases work with single-strand [[DNA]] and β helicases work with double-strand [[DNA]]. They are also classified by translocation polarity. If translocation occurs 3’-5’ the helicase is type A; if translocation occurs 5’-3’ it is type B.<ref name="singleton"/>

*'''Superfamily 1 (SF1)''': This superfamily can be further subdivided into SF1A and SF1B helicases.<ref name="singleton"/> In this group helicases can have either 3’-5’ (SF1A subfamily) or 5’-3’(SF1B subfamily) translocation polarity.<ref name="singleton"/><ref name="Stelter">{{cite journal | vauthors = Stelter M, Acajjaoui S, McSweeney S, Timmins J | title = Structural and mechanistic insight into DNA unwinding by Deinococcus radiodurans UvrD | journal = PLOS ONE | volume = 8 | issue = 10 | pages = e77364 | year = 2013 | pmid = 24143224 | pmc = 3797037 | doi = 10.1371/journal.pone.0077364 | doi-access = free | bibcode = 2013PLoSO...877364S }}</ref> The most known SF1A helicases are Rep and [[UvrABC endonuclease|UvrD]] in [[gram-negative]] bacteria and PcrA helicase from [[gram-positive]] bacteria.<ref name="singleton"/> The most known Helicases in the SF1B group are RecD and Dda helicases.<ref name="singleton"/> They have a RecA-like-fold core.<ref name="Fairman"/>
* '''Superfamily 2 (SF2)''': This is the largest group of helicases that are involved in varied cellular processes.<ref name="singleton"/><ref name="Umate"/> They are characterized by the presence of nine conserved motifs: Q, I, Ia, Ib, and II through VI.<ref name="Umate"/> This group is mainly composed of DEAD-box RNA helicases.<ref name="Fairman"/> Some other helicases included in SF2 are the RecQ-like family and the Snf2-like enzymes.<ref name="singleton"/> Most of the SF2 helicases are type A with a few exceptions such as the XPD family.<ref name="singleton"/> They have a RecA-like-fold core.<ref name="Fairman"/>
* '''Superfamily 3 (SF3)''': Superfamily 3 consists of AAA+ helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses.<ref name="PUB00033628">{{cite journal | vauthors = Iyer LM, Aravind L, Koonin EV | title = Common origin of four diverse families of large eukaryotic DNA viruses | journal = Journal of Virology | volume = 75 | issue = 23 | pages = 11720–11734 | date = December 2001 | pmid = 11689653 | pmc = 114758 | doi = 10.1128/JVI.75.23.11720-11734.2001 }}</ref><ref name="PUB00014778">{{cite journal | vauthors = Iyer LM, Leipe DD, Koonin EV, Aravind L | title = Evolutionary history and higher order classification of AAA+ ATPases | journal = Journal of Structural Biology | volume = 146 | issue = 1–2 | pages = 11–31 | year = 2004 | pmid = 15037234 | doi = 10.1016/j.jsb.2003.10.010 }}</ref> They have a 3’-5’ translocation directionality, meaning that they are all type A helicases.<ref name="singleton"/> The most known SF3 helicase is the papilloma virus E1 helicase.<ref name="singleton"/>
* '''Superfamily 4 (SF4)''': All SF4 family helicases have a type B polarity (5’-3’). They have a RecA fold.<ref name="singleton"/> The most studied SF4 helicase is gp4 from bacteriophage T7.<ref name="singleton"/>
* '''Superfamily 5 (SF5)''': [[Rho factor|Rho]] proteins conform the SF5 group. They have a RecA fold.<ref name="singleton"/>
* '''Superfamily 6 (SF6)''': They contain the core AAA+ that is not included in the SF3 classification.<ref name="singleton"/> Some proteins in the SF6 group are: mini chromosome maintenance [[minichromosome maintenance|MCM]], RuvB, RuvA, and RuvC.<ref name="singleton"/>

All helicases are members of a P-loop, or [[Walker motifs|Walker motif]]-containing family.

== Helicase disorders and diseases ==

=== ATRX helicase mutations ===
The ''[[ATRX]]'' gene encodes the ATP-dependent helicase, ATRX (also known as XH2 and XNP) of the SNF2 subgroup family, that is thought to be responsible for functions such as chromatin remodeling, gene regulation, and DNA methylation.<ref name="ropers">{{cite journal | vauthors = Ropers HH, Hamel BC | title = X-linked mental retardation | journal = Nature Reviews. Genetics | volume = 6 | issue = 1 | pages = 46–57 | date = January 2005 | pmid = 15630421 | doi = 10.1038/nrg1501 | s2cid = 427210 }}</ref><ref name="gibbons1995">{{cite journal | vauthors = Gibbons RJ, Picketts DJ, Villard L, Higgs DR | title = Mutations in a putative global transcriptional regulator cause X-linked mental retardation with alpha-thalassemia (ATR-X syndrome) | journal = Cell | volume = 80 | issue = 6 | pages = 837–845 | date = March 1995 | pmid = 7697714 | doi = 10.1016/0092-8674(95)90287-2 | doi-access = free }}</ref><ref name="nextprot">Nextprot Online Protein Database. [http://www.nextprot.org/db/entry/NX_P46100 " ATRX-Transcriptional regulator ATRX."], Retrieved on 12 November 2012.</ref><ref name="picketts">{{cite journal | vauthors = Picketts DJ, Higgs DR, Bachoo S, Blake DJ, Quarrell OW, Gibbons RJ | title = ATRX encodes a novel member of the SNF2 family of proteins: mutations point to a common mechanism underlying the ATR-X syndrome | journal = Human Molecular Genetics | volume = 5 | issue = 12 | pages = 1899–1907 | date = December 1996 | pmid = 8968741 | doi = 10.1093/hmg/5.12.1899 | doi-access = free }}</ref> These functions assist in prevention of apoptosis, resulting in cortical size regulation, as well as a contribution to the survival of hippocampal and cortical structures, affecting memory and learning.<ref name="ropers" /> This helicase is located on the X chromosome (Xq13.1-q21.1), in the pericentromeric heterochromatin and binds to [[heterochromatin protein 1]].<ref name="ropers" /><ref name="nextprot" /> Studies have shown that ATRX plays a role in rDNA methylation and is essential for embryonic development.<ref name="gibbons 2006">{{cite journal | vauthors = Gibbons R | title = Alpha thalassaemia-mental retardation, X linked | journal = Orphanet Journal of Rare Diseases | volume = 1 | pages = 15 | date = May 2006 | pmid = 16722615 | pmc = 1464382 | doi = 10.1186/1750-1172-1-15 | doi-access = free }}</ref> Mutations have been found throughout the ''ATRX'' protein, with over 90% of them being located in the zinc finger and helicase domains.<ref name="pagon">{{cite journal | vauthors = Stevenson RE | title = Alpha-Thalassemia X-Linked Intellectual Disability Syndrome | veditors =  Adam MP, Everman DB, Mirzaa GM, Pagon RA, Wallace SE, Bean LJ, Gripp KW, Amemiya A | journal = GeneReviews | year = 1993 | pmid = 20301622 | location = Seattle (WA) | publisher = University of Washington, Seattle }}</ref> Mutations of ATRX can result in X-linked-alpha-thalassaemia-mental retardation ([[ATR-X syndrome]]).<ref name="ropers" />

Various types of mutations found in ATRX have been found to be associated with ATR-X, including most commonly single-base missense mutations, as well as nonsense, frameshift, and deletion mutations.<ref name="picketts" /> Characteristics of ATR-X include: microcephaly, skeletal and facial abnormalities, mental retardation, genital abnormalities, seizures, limited language use and ability, and alpha-thalassemia.<ref name="ropers" /><ref name="gibbons 2006"/><ref name="gibbons1995"/> The phenotype seen in ATR-X suggests that the mutation of ATRX gene causes the downregulation of gene expression, such as the alpha-globin genes.<ref name="gibbons1995" /> It is still unknown what causes the expression of the various characteristics of ATR-X in different patients.<ref name="gibbons 2006"/>

=== XPD helicase point mutations ===
[[ERCC2|XPD]] (Xeroderma pigmentosum factor D, also known as protein ERCC2) is a 5'-3', Superfamily II, ATP-dependent helicase containing iron-sulphur cluster domains.<ref name=singleton/><ref name=rudolf>{{cite journal | vauthors = Rudolf J, Rouillon C, Schwarz-Linek U, White MF | title = The helicase XPD unwinds bubble structures and is not stalled by DNA lesions removed by the nucleotide excision repair pathway | journal = Nucleic Acids Research | volume = 38 | issue = 3 | pages = 931–941 | date = January 2010 | pmid = 19933257 | pmc = 2817471 | doi = 10.1093/nar/gkp1058 }}</ref> Inherited point mutations in XPD helicase have been shown to be associated with accelerated aging disorders such as [[Cockayne syndrome]] (CS) and [[trichothiodystrophy]] (TTD).<ref name=fan>{{cite journal | vauthors = Fan L, Fuss JO, Cheng QJ, Arvai AS, Hammel M, Roberts VA, Cooper PK, Tainer JA | display-authors = 6 | title = XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations | journal = Cell | volume = 133 | issue = 5 | pages = 789–800 | date = May 2008 | pmid = 18510924 | pmc = 3055247 | doi = 10.1016/j.cell.2008.04.030 }}</ref> Cockayne syndrome and trichothiodystrophy are both developmental disorders involving sensitivity to UV light and premature aging, and Cockayne syndrome exhibits severe mental retardation from the time of birth.<ref name="fan" /> The XPD helicase mutation has also been implicated in [[xeroderma pigmentosum]] (XP), a disorder characterized by sensitivity to UV light and resulting in a several 1000-fold increase in the development of skin cancer.<ref name="fan" />

XPD is an essential component of the [[TFIIH]] complex, a transcription and repair factor in the cell.<ref name="fan" /><ref name=laine>{{cite book | vauthors = Lainé JP, Mocquet V, Egly JM | title = DNA Repair, Part A | chapter = TFIIH enzymatic activities in transcription and nucleotide excision repair | series = Methods in Enzymology | volume = 408 | pages = 246–263 | year = 2006 | pmid = 16793373 | doi = 10.1016/S0076-6879(06)08015-3 | isbn = 9780121828134 }}</ref><ref name=tirode>{{cite journal | vauthors = Tirode F, Busso D, Coin F, Egly JM | title = Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7 | journal = Molecular Cell | volume = 3 | issue = 1 | pages = 87–95 | date = January 1999 | pmid = 10024882 | doi = 10.1016/S1097-2765(00)80177-X | doi-access = free }}</ref><ref name=sung>{{cite journal | vauthors = Sung P, Bailly V, Weber C, Thompson LH, Prakash L, Prakash S | title = Human xeroderma pigmentosum group D gene encodes a DNA helicase | journal = Nature | volume = 365 | issue = 6449 | pages = 852–855 | date = October 1993 | pmid = 8413672 | doi = 10.1038/365852a0 | s2cid = 4334960 | bibcode = 1993Natur.365..852S }}</ref><ref name=schaeffer>{{cite journal | vauthors = Schaeffer L, Roy R, Humbert S, Moncollin V, Vermeulen W, Hoeijmakers JH, Chambon P, Egly JM | display-authors = 6 | title = DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor | journal = Science | volume = 260 | issue = 5104 | pages = 58–63 | date = April 1993 | pmid = 8465201 | doi = 10.1126/science.8465201 | bibcode = 1993Sci...260...58S }}</ref> As part of this complex, it facilitates [[nucleotide excision repair]] by unwinding DNA.<ref name="fan" /> TFIIH assists in repairing damaged DNA such as sun damage.<ref name="fan" /><ref name="laine" /><ref name="tirode" /><ref name="sung" /><ref name="schaeffer" /> A mutation in the XPD helicase that helps form this complex and contributes to its function causes the sensitivity to sunlight seen in all three diseases, as well as the increased risk of cancer seen in XP and premature aging seen in trichothiodystrophy and Cockayne syndrome.<ref name="fan" />

XPD helicase mutations leading to trichothiodystrophy are found throughout the protein in various locations involved in protein-protein interactions.<ref name="fan" /> This mutation results in an unstable protein due to its inability to form stabilizing interactions with other proteins at the points of mutations.<ref name="fan" /> This, in turn, destabilizes the entire TFIIH complex, which leads to defects with transcription and repair mechanisms of the cell.<ref name="fan" />

It has been suggested that XPD helicase mutations leading to Cockayne syndrome could be the result of mutations within XPD, causing rigidity of the protein and subsequent inability to switch from repair functions to transcription functions due to a "locking" in repair mode.<ref name="fan" /> This could cause the helicase to cut DNA segments meant for transcription.<ref name="fan" /> Although current evidence points to a defect in the XPD helicase resulting in a loss of flexibility in the protein in cases of Cockayne syndrome, it is still unclear how this protein structure leads to the symptoms described in Cockayne syndrome.<ref name="fan" />

In xeroderma pigmentosa, the XPD helicase mutation exists at the site of ATP or DNA binding.<ref name="fan" /> This results in a structurally functional helicase able to facilitate transcription, however it inhibits its function in unwinding DNA and DNA repair.<ref name="fan" /> The lack of a cell's ability to repair mutations, such as those caused by sun damage, is the cause of the high cancer rate in xeroderma pigmentosa patients.

=== RecQ family mutations ===
[[File:RecQ helicase.png|thumb|right |RecQ helicase]]
[[RecQ helicase]]s (3'-5') belong to the Superfamily II group of helicases, which help to maintain stability of the genome and suppress inappropriate recombination.<ref name=hanada>{{cite journal | vauthors = Hanada K, Hickson ID | title = Molecular genetics of RecQ helicase disorders | journal = Cellular and Molecular Life Sciences | volume = 64 | issue = 17 | pages = 2306–2322 | date = September 2007 | pmid = 17571213 | doi = 10.1007/s00018-007-7121-z | s2cid = 29287970 | pmc = 11136437 }}</ref><ref name=opresko>{{cite journal | vauthors = Opresko PL, Cheng WH, Bohr VA | title = Junction of RecQ helicase biochemistry and human disease | journal = The Journal of Biological Chemistry | volume = 279 | issue = 18 | pages = 18099–18102 | date = April 2004 | pmid = 15023996 | doi = 10.1074/jbc.R300034200 | doi-access = free }}</ref> Deficiencies and/or mutations in RecQ family helicases display aberrant genetic recombination and/or DNA replication, which leads to chromosomal instability and an overall decreased ability to proliferate.<ref name="hanada" /> Mutations in RecQ family helicases BLM, [[RECQL4]], and WRN, which play a role in regulating homologous recombination, have been shown to result in the autosomal recessive diseases [[Bloom syndrome]] (BS), [[Rothmund–Thomson syndrome]] (RTS), and [[Werner syndrome]] (WS), respectively.<ref name="opresko" /><ref name=ouyang>{{cite journal | vauthors = Ouyang KJ, Woo LL, Ellis NA | title = Homologous recombination and maintenance of genome integrity: cancer and aging through the prism of human RecQ helicases | journal = Mechanisms of Ageing and Development | volume = 129 | issue = 7–8 | pages = 425–440 | year = 2008 | pmid = 18430459 | doi = 10.1016/j.mad.2008.03.003 | s2cid = 6804631 }}</ref>

Bloom syndrome is characterized by a predisposition to cancer with early onset, with a mean age-of-onset of 24 years.<ref name="opresko" /><ref name=ellis>{{cite journal | vauthors = Ellis NA, Groden J, Ye TZ, Straughen J, Lennon DJ, Ciocci S, Proytcheva M, German J | display-authors = 6 | title = The Bloom's syndrome gene product is homologous to RecQ helicases | journal = Cell | volume = 83 | issue = 4 | pages = 655–666 | date = November 1995 | pmid = 7585968 | doi = 10.1016/0092-8674(95)90105-1 | doi-access = free }}</ref> Cells of Bloom syndrome patients show a high frequency of reciprocal exchange between sister chromatids (SCEs) and excessive chromosomal damage.<ref name=selak>{{cite journal | vauthors = Selak N, Bachrati CZ, Shevelev I, Dietschy T, van Loon B, Jacob A, Hübscher U, Hoheisel JD, Hickson ID, Stagljar I | display-authors = 6 | title = The Bloom's syndrome helicase (BLM) interacts physically and functionally with p12, the smallest subunit of human DNA polymerase delta | journal = Nucleic Acids Research | volume = 36 | issue = 16 | pages = 5166–5179 | date = September 2008 | pmid = 18682526 | pmc = 2532730 | doi = 10.1093/nar/gkn498 }}</ref> There is evidence to suggest that BLM plays a role in rescuing disrupted DNA replication at replication forks.<ref name="selak" />

Werner syndrome is a disorder of premature aging, with symptoms including early onset of atherosclerosis and osteoporosis and other age related diseases, a high occurrence of sarcoma, and death often occurring from myocardial infarction or cancer in the 4th to 6th decade of life.<ref name="opresko" /><ref name=gray>{{cite journal | vauthors = Gray MD, Shen JC, Kamath-Loeb AS, Blank A, Sopher BL, Martin GM, Oshima J, Loeb LA | display-authors = 6 | title = The Werner syndrome protein is a DNA helicase | journal = Nature Genetics | volume = 17 | issue = 1 | pages = 100–103 | date = September 1997 | pmid = 9288107 | doi = 10.1038/ng0997-100 | s2cid = 20587915 }}</ref> Cells of Werner syndrome patients exhibit a reduced reproductive lifespan with chromosomal breaks and translocations, as well as large deletions of chromosomal components, causing genomic instability.<ref name="gray" />

Rothmund-Thomson syndrome, also known as [[poikiloderma congenitale]], is characterized by premature aging, skin and skeletal abnormalities, rash, [[poikiloderma]], juvenile cataracts, and a predisposition to cancers such as osteosarcomas.<ref name="opresko" /><ref name=kitao>{{cite journal | vauthors = Kitao S, Shimamoto A, Goto M, Miller RW, Smithson WA, Lindor NM, Furuichi Y | title = Mutations in RECQL4 cause a subset of cases of Rothmund-Thomson syndrome | journal = Nature Genetics | volume = 22 | issue = 1 | pages = 82–84 | date = May 1999 | pmid = 10319867 | doi = 10.1038/8788 | s2cid = 195211275 }}</ref> Chromosomal rearrangements causing genomic instability are found in the cells of Rothmund-Thomson syndrome patients. RecQ is a family of DNA helicase enzymes that are found in various organisms including bacteria, archaea, and eukaryotes (like humans). These enzymes play important roles in DNA metabolism during DNA replication, recombination, and repair. There are five known RecQ helicase proteins in humans: RecQ1, BLM, WRN, RecQ4, and RecQ5. Mutations in some of these genes are associated with genetic disorders. For instance, mutations in the BLM gene cause Bloom syndrome, which is characterized by increased cancer risk and other health issues.<ref>{{Cite journal |last1=Gupta |first1=Sonia Vidushi |last2=Schmidt |first2=Kristina Hildegard |date=2020-02-18 |title=Maintenance of Yeast Genome Integrity by RecQ Family DNA Helicases |journal=Genes |language=en |volume=11 |issue=2 |pages=205 |doi=10.3390/genes11020205 |issn=2073-4425 |pmc=7074392 |pmid=32085395 |doi-access=free }}</ref> Mutations in the WRN gene lead to Werner syndrome, a condition characterized by premature aging and an increased risk of age-related diseases. RecQ helicases are crucial for maintaining genomic stability and integrity. They help prevent the accumulation of genetic abnormalities that can lead to diseases like cancer. Genome integrity depends on the RecQ DNA helicase family, which includes DNA repair, recombination, replication, and transcription processes. Genome instability and early aging are conditions that arise from mutations in human RecQ helicases.<ref>{{Cite journal |last=Debnath S., Sharma S. RECQ1 Helicase in Genomic Stability and Cancer. Genes. 2020:11. doi: 10.3390/genes11060622] |first=Debnath S., Sharma S. RECQ1 Helicase in Genomic Stability and Cancer. Genes. 2020:11. doi: 10.3390/genes11060622] |author-link= |date= |title= |url= |journal=}}</ref> RecQ helicase Sgs1 is missing in yeast cells, making them useful models for comprehending human cell abnormalities and the RecQ helicase function.<ref>{{Cite journal |last1=Hendrickson |first1=W. A. |last2=Ward |first2=K. B. |date=1975-10-27 |title=Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin |url=https://pubmed.ncbi.nlm.nih.gov/5 |journal=Biochemical and Biophysical Research Communications |volume=66 |issue=4 |pages=1349–1356 |doi=10.1016/0006-291x(75)90508-2 |issn=1090-2104 |pmid=5}}</ref> The RecQ helicase family member, RECQ1, is connected to a small number of uncommon genetic cancer disorders in individuals. It participates in transcription, the cell cycle, and DNA repair. According to recent research, missense mutations in the RECQ1 gene may play a role in the development of familial breast cancer. DNA helicases are frequently attracted to regions of DNA damage and are essential for cellular DNA replication, recombination, repair, and transcription. Chemical manipulation of their molecular processes can change the rate at which cancer cells divide, as well as, the efficiency of transactions and cellular homeostasis. Small-molecule-induced entrapment of DNA helicases, a type of DNA metabolic protein, may have deleterious consequences on rapidly proliferating cancer cells, which could be effective in cancer treatment.

During [[meiosis]] DNA double-strand breaks and other [[DNA damage (naturally occurring)|DNA damage]]s in a [[chromatid]] are repaired by [[homologous recombination]] using either the [[sister chromatids|sister chromatid]] or a homologous non-sister chromatid as template.  This repair can result in a [[chromosomal crossover|crossover]] (CO) or, more frequently, a non-crossover (NCO) recombinant.  In the yeast ''[[Schizosaccharomyces pombe]]'' the [[FANCM]]-family DNA helicase FmI1 directs NCO recombination formation during meiosis.<ref name="pmid22723423">{{cite journal | vauthors = Lorenz A, Osman F, Sun W, Nandi S, Steinacher R, Whitby MC | title = The fission yeast FANCM ortholog directs non-crossover recombination during meiosis | journal = Science | volume = 336 | issue = 6088 | pages = 1585–1588 | date = June 2012 | pmid = 22723423 | pmc = 3399777 | doi = 10.1126/science.1220111 | bibcode = 2012Sci...336.1585L }}</ref>  The [[RecQ helicase|RecQ-type helicase]] Rqh1 also directs NCO meiotic recombination.<ref name="pmid25414342">{{cite journal | vauthors = Lorenz A, Mehats A, Osman F, Whitby MC | title = Rad51/Dmc1 paralogs and mediators oppose DNA helicases to limit hybrid DNA formation and promote crossovers during meiotic recombination | journal = Nucleic Acids Research | volume = 42 | issue = 22 | pages = 13723–13735 | date = December 2014 | pmid = 25414342 | pmc = 4267644 | doi = 10.1093/nar/gku1219 }}</ref>  These helicases, through their ability to unwind [[D-loop]] intermediates, promote NCO recombination by the process of [[synthesis-dependent strand annealing]].

In the plant ''[[Arabidopsis thaliana]]'', FANCM helicase promotes NCO and antagonizes the formation of CO recombinants.<ref name="pmid25825745">{{cite journal | vauthors = Séguéla-Arnaud M, Crismani W, Larchevêque C, Mazel J, Froger N, Choinard S, Lemhemdi A, Macaisne N, Van Leene J, Gevaert K, De Jaeger G, Chelysheva L, Mercier R | display-authors = 6 | title = Multiple mechanisms limit meiotic crossovers: TOP3α and two BLM homologs antagonize crossovers in parallel to FANCM | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 15 | pages = 4713–4718 | date = April 2015 | pmid = 25825745 | pmc = 4403193 | doi = 10.1073/pnas.1423107112 | doi-access = free | bibcode = 2015PNAS..112.4713S }}</ref>  Another helicase, RECQ4A/B, also independently reduces COs.  It was suggested that COs are restricted because of the long term costs of CO recombination, that is, the breaking up of favourable genetic combinations of alleles built up by past [[natural selection]].<ref name="pmid25825745" />

== RNA helicases ==
[[File:Human DEAD-box RNA helicase.jpg|thumb|right|Human DEAD-box RNA helicase]]
[[File:DEAD box Accessory Domains.png|thumb|left| alt=A| This image represents the different promoter sequences and accessory domains that aid in RNA unwinding (local strand separation). The regions in red are ATP binding domains and the regions in yellow are RNA interaction domains. Specific sequences termed DEAD box proteins are also present that help catalyze reactions in which ATP does not need to be directly hydrolyzed, as long as it binds to the domains on the strand.]]

RNA helicases are essential for most processes of RNA metabolism such as [[ribosome]] biogenesis, pre-mRNA splicing, and [[translation (biology)|translation]] initiation. They also play an important role in sensing viral RNAs.<ref name="rnadatabase" /> RNA helicases are involved in the mediation of antiviral immune response because they can identify foreign RNAs in vertebrates. About 80% of all viruses are RNA viruses and they contain their own RNA helicases.<ref name="rnavirus">{{cite journal | vauthors = Steimer L, Klostermeier D | title = RNA helicases in infection and disease | journal = RNA Biology | volume = 9 | issue = 6 | pages = 751–771 | date = June 2012 | pmid = 22699555 | doi = 10.4161/rna.20090 | doi-access = free }}</ref> Defective RNA helicases have been linked to cancers, infectious diseases and neuro-degenerative disorders.<ref name="rnadatabase" /> Some neurological disorders associated with defective RNA helicases are: [[amyotrophic lateral sclerosis]], [[spinal muscular atrophy]], [[spinocerebellar ataxia|spinocerebellar ataxia type-2]], [[Alzheimer disease]], and [[lethal congenital contracture syndrome]].<ref name="rnavirus" />

RNA helicases and DNA helicases can be found together in all the helicase superfamilies except for SF6.<ref name="isbn1-84755-914-X">{{cite book | veditors = Jankowsky E |title= RNA Helicases (RSC Biomolecular Sciences) |publisher= Royal Society of Chemistry |location= Cambridge, England |year= 2010 |page= 5 |isbn= 978-1-84755-914-2 |chapter= An introduction to RNA helicases: superfamilies, families, and major themes |vauthors=Jankowsky E, Fairman-Williams ME }}</ref><ref name="rnahelicases">{{cite journal | vauthors = Ranji A, Boris-Lawrie K | title = RNA helicases: emerging roles in viral replication and the host innate response | journal = RNA Biology | volume = 7 | issue = 6 | pages = 775–787 | year = 2010 | pmid = 21173576 | pmc = 3073335 | doi = 10.4161/rna.7.6.14249 }}</ref> All the eukaryotic RNA helicases that have been identified up to date are non-ring forming and are part of SF1 and SF2. On the other hand, ring-forming RNA helicases have been found in bacteria and viruses.<ref name="rnadatabase" /> However, not all RNA helicases exhibit helicase activity as defined by enzymatic function, i.e., proteins of the Swi/Snf family. Although these proteins carry the typical helicase motifs, hydrolize ATP in a nucleic acid-dependent manner, and are built around a helicase core, in general, no unwinding activity is observed.<ref name="pmid20813532">{{cite journal | vauthors = Jankowsky E | title = RNA helicases at work: binding and rearranging | journal = Trends in Biochemical Sciences | volume = 36 | issue = 1 | pages = 19–29 | date = January 2011 | pmid = 20813532 | pmc = 3017212 | doi = 10.1016/j.tibs.2010.07.008 }}</ref>

RNA helicases that do exhibit unwinding activity have been characterized by at least two different mechanisms: canonical duplex unwinding and local strand separation. Canonical duplex unwinding is the stepwise directional separation of a duplex strand, as described above, for DNA unwinding. However, local strand separation occurs by a process wherein the helicase enzyme is loaded at any place along the duplex. This is usually aided by a single-strand region of the RNA, and the loading of the enzyme is accompanied with ATP binding.<ref name="pmid17964264">{{cite journal | vauthors = Yang Q, Del Campo M, Lambowitz AM, Jankowsky E | title = DEAD-box proteins unwind duplexes by local strand separation | journal = Molecular Cell | volume = 28 | issue = 2 | pages = 253–263 | date = October 2007 | pmid = 17964264 | doi = 10.1016/j.molcel.2007.08.016 | doi-access = free }}</ref> Once the helicase and ATP are bound, local strand separation occurs, which requires binding of ATP but not the actual process of ATP hydrolysis.<ref name="pmid19088201">{{cite journal | vauthors = Liu F, Putnam A, Jankowsky E | title = ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 51 | pages = 20209–20214 | date = December 2008 | pmid = 19088201 | pmc = 2629341 | doi = 10.1073/pnas.0811115106 | doi-access = free | bibcode = 2008PNAS..10520209L }}</ref> Presented with fewer base pairs the duplex then dissociates without further assistance from the enzyme. This mode of unwinding is used by the [[DEAD/DEAH box helicase]]s.<ref name="pmid21297876">{{cite journal | vauthors = Jarmoskaite I, Russell R | title = DEAD-box proteins as RNA helicases and chaperones | journal = Wiley Interdisciplinary Reviews. RNA | volume = 2 | issue = 1 | pages = 135–152 | year = 2011 | pmid = 21297876 | pmc = 3032546 | doi = 10.1002/wrna.50 }}</ref>

An RNA helicase database<ref>{{cite web|url=http://www.rnahelicase.org/|title=Index of /|website=www.rnahelicase.org|access-date=2012-12-07|archive-url=https://web.archive.org/web/20141218021806/http://rnahelicase.org/|archive-date=2014-12-18|url-status=dead}}</ref> is currently available online that contains a comprehensive list of RNA helicases with information such as sequence, structure, and biochemical and cellular functions.<ref name=rnadatabase>{{cite journal | vauthors = Jankowsky A, Guenther UP, Jankowsky E | title = The RNA helicase database | journal = Nucleic Acids Research | volume = 39 | issue = Database issue | pages = D338–D341 | date = January 2011 | pmid = 21112871 | pmc = 3013637 | doi = 10.1093/nar/gkq1002 }}</ref>

== Diagnostic tools for helicase measurement ==

=== Measuring and monitoring helicase activity ===
Various methods are used to measure helicase activity ''in vitro''. These methods range from assays that are qualitative (assays that usually entail results that do not involve values or measurements) to quantitative (assays with numerical results that can be utilized in statistical and numerical analysis). In 1982–1983, the first direct biochemical assay was developed for measuring helicase activity.<ref name="Venkatesan_1982" /><ref name="pmid6315716">{{cite journal | vauthors = Matson SW, Tabor S, Richardson CC | title = The gene 4 protein of bacteriophage T7. Characterization of helicase activity | journal = The Journal of Biological Chemistry | volume = 258 | issue = 22 | pages = 14017–14024 | date = November 1983 | pmid = 6315716 | doi = 10.1016/S0021-9258(17)44018-X | doi-access = free }}</ref> This method was called a "strand displacement assay".
* Strand displacement assay involves the [[radiolabeling]] of DNA duplexes. Following helicase treatment, the single-strand DNA is visually detected as separate from the double-strand DNA by non-denaturing [[PAGE|PAGE electrophoresis]]. Following detection of the single-strand DNA, the amount of radioactive tag that is on the single-strand DNA is quantified to give a numerical value for the amount of double-strand DNA unwinding.{{pb}}The strand displacement assay is acceptable for qualitative analysis, its inability to display results for more than a single time point, its time consumption, and its dependence on radioactive compounds for labeling warranted the need for development of diagnostics that can monitor helicase activity in real time.

Other methods were later developed that incorporated some, if not all of the following: high-throughput mechanics, the use of non-radioactive nucleotide labeling, faster reaction time/less time consumption, real-time monitoring of helicase activity (using kinetic measurement instead of endpoint/single point analysis). These methodologies include: "a rapid quench flow method, fluorescence-based assays, filtration assays, a [[scintillation proximity assay]], a time resolved [[fluorescence resonance energy transfer]] assay, an assay based on flashplate technology, homogenous time-resolved fluorescence quenching assays, and electrochemiluminescence-based helicase assays".<ref name="pmid15128294">{{cite journal | vauthors = Tuteja N, Tuteja R | title = Prokaryotic and eukaryotic DNA helicases. Essential molecular motor proteins for cellular machinery | journal = European Journal of Biochemistry | volume = 271 | issue = 10 | pages = 1835–1848 | date = May 2004 | pmid = 15128294 | pmc = 7164108 | doi = 10.1111/j.1432-1033.2004.04093.x }}</ref> With the use of specialized mathematical equations, some of these assays can be utilized to determine how many base paired nucleotides a helicase can break per hydrolysis of 1 ATP molecule.<ref name="pmid22665805">{{cite journal | vauthors = Sarlós K, Gyimesi M, Kovács M | title = RecQ helicase translocates along single-stranded DNA with a moderate processivity and tight mechanochemical coupling | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 109 | issue = 25 | pages = 9804–9809 | date = June 2012 | pmid = 22665805 | pmc = 3382518 | doi = 10.1073/pnas.1114468109 | doi-access = free | bibcode = 2012PNAS..109.9804S }}</ref>

Commercially available diagnostic kits are also available. One such kit is the "Trupoint" diagnostic assay from [[PerkinElmer]], Inc. This assay is a time-resolved fluorescence quenching assay that utilizes the PerkinElmer "SignalClimb" technology that is based on two labels that bind in close proximity to one another but on opposite DNA strands. One label is a fluorescent lanthanide chelate, which serves as the label that is monitored through an adequate 96/384 well plate reader. The other label is an organic quencher molecule. The basis of this assay is the "quenching" or repressing of the lanthanide chelate signal by the organic quencher molecule when the two are in close proximity – as they would be when the DNA duplex is in its native state. Upon helicase activity on the duplex, the quencher and lanthanide labels get separated as the DNA is unwound. This loss in proximity negates the quenchers ability to repress the lanthanide signal, causing a detectable increase in fluorescence that is representative of the amount of unwound DNA and can be used as a quantifiable measurement of helicase activity.
The execution and use of single-molecule fluorescence imaging techniques, focusing on methods that include optical trapping in conjunction with epifluorescent imaging, and also surface immobilization in conjunction with total internal reflection fluorescence visualization. Combined with microchannel flow cells and microfluidic control, allow individual fluorescently labeled protein and DNA molecules to be imaged and tracked, affording measurement of DNA unwinding and translocation at single-molecule resolution.<ref>{{cite book | vauthors = Pavankumar TL, Exell JC, Kowalczykowski SC | title = Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods | chapter = Direct Fluorescent Imaging of Translocation and Unwinding by Individual DNA Helicases | series = Methods in Enzymology | volume = 581 | pages = 1–32 | date = 1 January 2016 | pmid = 27793277 | pmc = 5854184 | doi = 10.1016/bs.mie.2016.09.010 | isbn = 9780128092675 }}</ref>

=== Determining helicase polarity ===
Helicase polarity, which is also deemed "directionality", is defined as the direction (characterized as 5'→3' or 3'→5') of helicase movement on the DNA/RNA single-strand along which it is moving. This determination of polarity is vital in f.ex. determining whether the tested helicase attaches to the DNA leading strand, or the DNA lagging strand. To characterize this helicase feature, a partially duplex DNA is used as the substrate that has a central single-strand DNA region with different lengths of duplex regions of DNA (one short region that runs 5'→3' and one longer region that runs 3'→5') on both sides of this region.<ref>{{cite book | vauthors = Borowiec JA | chapter = DNA Helicases| veditors = DePamphilis ML | title = DNA Replication in Eukaryotic Cells. | date = 1996 | publisher = Cold Spring Harbor Laboratory Press | location = Cold Spring Harbor, NY | pages = 545–574 | isbn = 978-0-87969-459-3 | oclc = 246537432 }}</ref> Once the helicase is added to that central single-strand region, the polarity is determined by characterization on the newly formed single-strand DNA.

== See also ==
* [[Chromodomain]] helicase DNA binding protein: [[CHD1]], [[CHD1L]], [[CHD2]], [[CHD3]], [[CHD4]], [[CHD5]], [[CHD6]], [[CHD7]], [[CHD8]], [[CHD9]]
* [[DEAD box]]/[[DEAD/DEAH box helicase]]: [[DDX3X]], [[DDX5]], [[DDX6]], [[DDX10]], [[DDX11]], [[DDX12]], [[DDX58]], [[DHX8]], [[DHX9]], [[DHX37]], [[DHX40]], [[DHX58]]
* [[ASCC3]], [[BLM (gene)|BLM]], [[BRIP1]], [[DNA2 (gene)|DNA2]], [[FBXO18]], [[FBXO30]], [[HELB]], [[HELLS]], [[HELQ]], [[HELZ]], [[HFM1]], [[HLTF]], [[IFIH1]], [[NAV2]], [[PIF1]], [[RECQL]], [[RTEL1]], [[SHPRH]], [[SMARCA4]], [[SMARCAL1]], [[WRN (gene)|WRN]], [[WRNIP1]]
* [[RNA helicase database]]

== References ==
{{reflist|30em}}

== External links ==
{{Commons category|Helicases}}
* {{MeshName|DNA+Helicases}}
* {{MeshName|RNA+Helicases}}

{{DNA replication}}
{{DNA repair}}
{{Kinases}}
{{Acid anhydride hydrolases}}
{{Enzymes}}
{{Portal bar|Biology|border=no}}

[[Category:EC 3.6.4]]
[[Category:DNA replication]]
[[Category:Helicases]]