102:) usually use DNA primers, since they are more temperature stable. Primers can be designed in laboratory for specific reactions such as polymerase chain reaction (PCR). When designing PCR primers, there are specific measures that must be taken into consideration, like the melting temperature of the primers and the annealing temperature of the reaction itself. Moreover, the DNA binding sequence of the primer in vitro has to be specifically chosen, which is done using a method called basic local alignment search tool (BLAST) that scans the DNA and finds specific and unique regions for the primer to bind.
272:, in eukaryotes itβs known as the RNase H2. This enzyme degrades most of the annealed RNA primer, except the nucleotides close to the 5β end of the primer. Thus, the remaining nucleotides are displayed into a flap that is cleaved off using FEN-1. The last possible method of removing RNA primer is known as the long flap pathway. In this pathway several enzymes are recruited to elongate the RNA primer and then cleave it off. The flaps are elongated by a 5β to 3β
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371:(PCR) uses a pair of custom primers to direct DNA elongation toward each other at opposite ends of the sequence being amplified. These primers are typically between 18 and 24 bases in length and must code for only the specific upstream and downstream sites of the sequence being amplified. A primer that can bind to multiple regions along the DNA will amplify them all, eliminating the purpose of PCR.
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using an enzyme called ligase. The removal process of the RNA primer requires several enzymes, such as Fen1, Lig1, and others that work in coordination with DNA polymerase, to ensure the removal of the RNA nucleotides and the addition of DNA nucleotides. Living organisms use solely RNA primers, while laboratory techniques in
424:
Selecting a specific region of DNA for primer binding requires some additional considerations. Regions high in mononucleotide and dinucleotide repeats should be avoided, as loop formation can occur and contribute to mishybridization. Primers should not easily anneal with other primers in the mixture;
374:
A few criteria must be brought into consideration when designing a pair of PCR primers. Pairs of primers should have similar melting temperatures since annealing during PCR occurs for both strands simultaneously, and this shared melting temperature must not be either too much higher or lower than the
263:
are formed, which are discontinuous strands of DNA. Then, when the DNA polymerase reaches to the 5β end of the RNA primer from the previous
Okazaki fragment, it displaces the 5β² end of the primer into a single-stranded RNA flap which is removed by nuclease cleavage. Cleavage of the RNA flaps involves
81:
before DNA polymerase can begin a complementary strand. DNA polymerase adds nucleotides after binding to the RNA primer and synthesizes the whole strand. Later, the RNA strands must be removed accurately and replace them with DNA nucleotides forming a gap region known as a nick that is filled in
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As of 2014, many online tools are freely available for primer design, some of which focus on specific applications of PCR. Primers with high specificity for a subset of DNA templates in the presence of many similar variants can be designed using by some software (e.g.
425:
this phenomenon can lead to the production of 'primer dimer' products contaminating the end solution. Primers should also not anneal strongly to themselves, as internal hairpins and loops could hinder the annealing with the template DNA.
288:, which has a helicase-nuclease activity, that cleaves the long flap of RNA primer, which then leaves behind a couple of nucleotides that are cleaved by FEN1. At the end, when all the RNA primers have been removed, nicks form between the
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before being extended by DNA polymerase. The ability to create and customize synthetic primers has proven an invaluable tool necessary to a variety of molecular biological approaches involving the analysis of DNA. Both the
428:
When designing primers, additional nucleotide bases can be added to the back ends of each primer, resulting in a customized cap sequence on each end of the amplified region. One application for this practice is for use in
188:. Reverse transcriptase is an enzyme that uses a template strand of RNA to synthesize a complementary strand of DNA. The DNA polymerase component of reverse transcriptase requires an existing 3' end to begin synthesis.
235:
direction, and polymerase I can do these activities simultaneously; this is known as βNick
Translationβ. Nick translation refers to the synchronized activity of polymerase I in removing the RNA primer and adding
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Additionally, primer sequences need to be chosen to uniquely select for a region of DNA, avoiding the possibility of hybridization to a similar sequence nearby. A commonly used method for selecting a primer site is
536:. Differences among sequences are accounted for by using IUPAC degeneracies for individual bases. PCR primers are then synthesized as a mixture of primers corresponding to all permutations of the codon sequence.
475:. This allows different organisms to have a significantly different genetic sequence that code for a highly similar protein. For this reason, degenerate primers are also used when primer design is based on
268:(FEN-1), which cleaves the 5β overhanging flap. This method is known as the short flap pathway of RNA primer removal. The second way to cleave a RNA primer is by degrading the RNA strand using a
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Adenosine added on the primer 50 end improved TA cloning efficiency of polymerase chain reaction products, Ri-He Peng, Ai-Sheng Xiong, Jin-ge Liu, Fang Xu, Cai Bin, Hong Zhu, Quan-Hong Yao
173:
cannot add bases in the 3β²β5β² direction complementary to the template strand, DNA is synthesized βbackwardβ in short fragments moving away from the replication fork, known as
401:
search, whereby all the possible regions to which a primer may bind can be seen. Both the nucleotide sequence as well as the primer itself can be BLAST searched. The free
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or allow the recovery of genes from organisms where genomic information is not available. Usually, degenerate primers are designed by aligning gene sequencing found in
674:
177:. Unlike in the leading strand, this method results in the repeated starting and stopping of DNA synthesis, requiring multiple RNA primers. Along the DNA template,
284:(RPA). The RPA-bound DNA inhibits the activity or recruitment of FEN1, as a result another nuclease must be recruited to cleave the flap. This second nuclease is
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386:(melting temperature) too much higher than the reaction's annealing temperature may mishybridize and extend at an incorrect location along the DNA sequence. A
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In prokaryotes, DNA polymerase I synthesizes the
Okazaki fragment until it reaches the previous RNA primer. Then the enzyme simultaneously acts as a
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518:. Degenerate primers may not perfectly hybridize with a target sequence, which can greatly reduce the specificity of the PCR amplification.
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tool Primer-BLAST integrates primer design and BLAST search into one application, as do commercial software products such as ePrime and
153:. Starting from the free 3β-OH of the primer, known as the primer terminus, a DNA polymerase can extend a newly synthesized strand. The
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three methods of primer removal. The first possibility of primer removal is by creating a short flap that is directly removed by
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860:"New Sets of Primers for DNA Identification of Non-Indigenous Fish Species in the Volga-Kama Basin (European Russia)"
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These are mixtures of primers that are similar, but not identical. These may be convenient when amplifying the same
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Karabanov, D.P.; Bekker, E.I.; Pavlov, D.D.; Borovikova, E.A.; Kodukhova, Y.V.; Kotov, A.A. (1 February 2022).
165:, requiring only an initial RNA primer to begin synthesis. In the lagging strand, the template DNA runs in the
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is essential for the completion of replication. Thus, as the lagging strand being synthesized by
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intersperses RNA primers that DNA polymerase uses to synthesize DNA from in the 5β²β3β² direction.
604:"In vitro reconstitution of RNA primer removal in Archaea reveals the existence of two pathways"
459:, as the sequences are probably similar but not identical. This technique is useful because the
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then joins the fragmented strands together, completing the synthesis of the lagging strand.
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behind. Both the activities of polymerization and excision of the RNA primer occur in the
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significantly lower than the annealing temperature may fail to anneal and extend at all.
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to a specific site on the template DNA. In solution, the primer spontaneously
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Diagrammatic representation of the forward and reverse primers for a standard
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Short strand of RNA or DNA that serves as a starting point for DNA synthesis
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Doudna; Cox; O'Donnell, Jennifer; Michael M.; Michael (December 21, 2016).
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581:. New York: W. H. Freeman and Company. pp. 221β238, 369β376, 592β593.
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528:. They allow for the amplification of genes from thus far uncultivated
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69:(responsible for DNA replication) enzymes are only capable of adding
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Another example of primers being used to enable DNA synthesis is
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693:"Primer removal during mammalian mitochondrial DNA replication"
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of an existing nucleic acid, requiring a primer be bound to
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add a complementary RNA primer to the reading template
817:. NCBI - National Center for Biotechnology Information
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that fill the gaps where the RNA primer was present.
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Balakrishnan, Lata; Bambara, Robert A. (2013-02-01).
548:– the methods by which primers are manufactured
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are widely used and extremely useful in the field of
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The DNA replication fork. RNA primer labeled at top.
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409:. Computer simulations of theoretical PCR results (
334:Synthetic primers, sometimes known as oligos, are
53:used by all living organisms in the initiation of
247:In eukaryotes the removal of RNA primers in the
123:RNA primers are used by living organisms in the
691:Uhler, Jay P.; Falkenberg, Maria (2015-10-01).
327:. For possible methods involving primers, see
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338:, usually of DNA, which can be customized to
8:
673:: CS1 maint: multiple names: authors list (
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749:Cold Spring Harbor Perspectives in Biology
651:Molecular Biology: Principles and practice
579:Molecular Biology: Principles and Practice
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447:Some situations may call for the use of
323:For the organic chemistry involved, see
161:in one continuous piece moving with the
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336:chemically synthesized oligonucleotides
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266:flap structure-specific endonuclease 1
61:primer may also be referred to as an
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486:might be "ATH", where A stands for
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1976:Post-transcriptional modification
1602:Control of chromosome duplication
1168:Autonomously replicating sequence
839:. Wellcome Trust Sanger Institute
602:Henneke, Ghislaine (2012-09-26).
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1981:Post-translational modification
353:Sanger chain termination method
514:, using the IUPAC symbols for
1:
2103:Post-translational regulation
1325:DNA polymerase III holoenzyme
1175:Single-strand binding protein
745:"Okazaki fragment metabolism"
65:, short for oligonucleotide.
2051:High-throughput technique ("
710:10.1016/j.dnarep.2015.07.003
467:, meaning several different
135:. A class of enzymes called
49:is a short, single-stranded
1929:Functional biology/medicine
761:10.1101/cshperspect.a010173
300:, through a process called
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1421:Prokaryotic DNA polymerase
1122:Minichromosome maintenance
1069:Origin recognition complex
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346:with the template through
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112:
29:
2192:Polymerase chain reaction
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1499:Eukaryotic DNA polymerase
546:Oligonucleotide synthesis
369:polymerase chain reaction
348:Watson-Crick base pairing
325:Oligonucleotide synthesis
308:Uses of synthetic primers
296:using an enzyme known as
100:polymerase chain reaction
577:Cox, Michael M. (2015).
292:that are filled-in with
208:) and replaced with new
1062:Pre-replication complex
993:Pre-replication complex
196:After the insertion of
94:DNA synthesis (such as
471:can code for the same
320:
157:in DNA replication is
42:
1924:Developmental biology
1919:Computational biology
1485:Replication protein A
1254:Origin of replication
377:annealing temperature
315:
282:replication protein A
186:reverse transcription
113:Further information:
40:
2098:Post-transcriptional
1456:Replication factor C
329:Nucleic acid methods
294:deoxyribonucleotides
238:deoxyribonucleotides
229:deoxyribonucleotides
227:in front and adding
210:deoxyribonucleotides
30:For other uses, see
1893:Histone methylation
608:Biochemical Journal
506:, according to the
449:degenerate primers.
620:10.1042/BJ20120959
522:Degenerate primers
437:Degenerate primers
379:. A primer with a
321:
223:, removing primer
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2187:Molecular biology
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2126:Molecular biology
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2065:Mass spectrometry
1942:
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1709:Molecular biology
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1468:Flap endonuclease
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1285:Okazaki fragments
879:10.3390/w14030437
653:. W. H. Freeman.
526:microbial ecology
363:PCR primer design
290:Okazaki fragments
261:Okazaki fragments
221:5β²β3β² exonuclease
198:Okazaki fragments
175:Okazaki fragments
88:molecular biology
16:(Redirected from
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837:"About DECIPHER"
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167:5β²β3β² direction
151:lagging strands
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801:"Primer-BLAST"
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755:(2): a010173.
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441:Main article:
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249:lagging strand
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192:Primer removal
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171:DNA polymerase
155:leading strand
115:DNA polymerase
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96:DNA sequencing
67:DNA polymerase
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2061:
2058:
2054:
2049:
2048:
2045:
2044:Radioactivity
2041:
2037:
2034:
2030:
2027:
2025:
2022:
2021:
2019:
2016:
2012:
2009:
2007:
2004:
2003:
2001:
1997:
1991:
1987:
1984:
1982:
1979:
1977:
1974:
1972:
1969:
1967:
1964:
1962:
1961:Cultured meat
1959:
1958:
1956:
1952:
1949:
1945:
1935:
1932:
1930:
1927:
1925:
1922:
1920:
1917:
1915:
1912:
1910:
1907:
1906:
1904:
1900:
1894:
1891:
1889:
1886:
1882:
1881:trp repressor
1879:
1877:
1876:lac repressor
1874:
1873:
1872:
1869:
1867:
1864:
1862:
1859:
1857:
1854:
1852:
1849:
1845:
1842:
1840:
1837:
1835:
1832:
1831:
1830:
1827:
1823:
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1810:
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1801:
1796:
1795:
1794:
1793:
1791:
1787:
1780:
1776:
1773:
1770:
1766:
1765:Transcription
1763:
1760:
1756:
1753:
1752:
1750:
1748:
1747:Central dogma
1744:
1741:
1737:
1731:
1728:
1726:
1723:
1721:
1718:
1717:
1714:
1710:
1703:
1698:
1696:
1691:
1689:
1684:
1683:
1680:
1666:
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1647:
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1635:
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1613:
1609:
1603:
1600:
1599:
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1586:
1585:
1580:
1577:
1575:
1572:
1570:
1567:
1565:
1562:
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1560:
1557:
1553:
1550:
1548:
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1540:
1538:
1535:
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1530:
1526:
1523:
1521:
1518:
1516:
1513:
1511:
1508:
1507:
1506:
1503:
1500:
1497:
1496:
1491:
1488:
1487:
1486:
1483:
1481:
1480:Topoisomerase
1478:
1474:
1471:
1470:
1469:
1466:
1462:
1459:
1458:
1457:
1454:
1453:
1451:
1448:
1439:
1431:
1428:
1427:
1426:
1422:
1419:
1418:
1413:
1410:
1409:
1408:
1407:Topoisomerase
1405:
1403:
1400:
1398:
1395:
1393:
1390:
1386:
1383:
1381:
1378:
1376:
1373:
1371:
1368:
1366:
1363:
1361:
1358:
1356:
1353:
1351:
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1333:
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1328:
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1317:
1310:
1307:
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1301:
1291:
1288:
1286:
1283:
1279:
1275:
1272:
1271:
1270:
1267:
1266:
1263:
1259:
1255:
1252:
1251:
1249:
1245:
1239:
1236:
1234:
1230:
1227:
1226:
1223:
1219:
1216:
1215:
1210:
1207:
1205:
1202:
1201:
1200:
1197:
1196:
1191:
1188:
1186:
1183:
1181:
1178:
1177:
1176:
1173:
1172:
1169:
1166:
1165:
1162:
1159:
1158:
1153:
1150:
1148:
1145:
1143:
1140:
1138:
1135:
1133:
1130:
1128:
1125:
1124:
1123:
1120:
1119:
1116:
1113:
1112:
1109:
1106:
1105:
1100:
1097:
1095:
1092:
1090:
1087:
1085:
1082:
1080:
1077:
1075:
1072:
1071:
1070:
1067:
1066:
1063:
1060:
1059:
1057:
1054:
1045:
1037:
1034:
1033:
1032:
1029:
1028:
1023:
1020:
1018:
1015:
1013:
1010:
1009:
1008:
1005:
1004:
1001:
998:
997:
994:
991:
990:
988:
985:
978:
975:
973:
969:
964:
960:
956:
949:
944:
942:
937:
935:
930:
929:
926:
920:
917:
915:
912:
911:
907:
897:
894:
889:
885:
880:
875:
871:
867:
866:
861:
854:
851:
838:
832:
829:
816:
810:
807:
802:
796:
793:
788:
784:
779:
774:
770:
766:
762:
758:
754:
750:
746:
739:
737:
733:
728:
724:
720:
716:
711:
706:
702:
698:
694:
687:
685:
681:
676:
670:
662:
660:9781319116378
656:
652:
645:
642:
637:
633:
629:
625:
621:
617:
613:
609:
605:
598:
595:
590:
588:9781464126147
584:
580:
573:
571:
569:
567:
565:
563:
559:
552:
547:
544:
543:
539:
537:
535:
531:
527:
523:
519:
517:
513:
509:
505:
501:
497:
493:
489:
485:
482:
478:
474:
470:
466:
462:
458:
454:
450:
444:
436:
434:
432:
426:
422:
420:
414:
412:
408:
404:
400:
394:
389:
382:
378:
372:
370:
362:
360:
358:
354:
349:
345:
341:
337:
330:
326:
319:
314:
307:
305:
303:
299:
295:
291:
287:
286:DNA2 nuclease
283:
279:
275:
271:
267:
262:
258:
254:
250:
245:
243:
239:
234:
230:
226:
222:
217:
215:
211:
207:
203:
199:
191:
189:
187:
182:
180:
176:
172:
168:
164:
160:
156:
152:
148:
144:
143:
138:
134:
130:
126:
120:
116:
109:
105:
103:
101:
97:
93:
90:that require
89:
85:
80:
76:
72:
68:
64:
60:
56:
55:DNA synthesis
52:
48:
39:
33:
19:
2136:
2124:
2036:Fluorescence
2024:Nucleic acid
2015:C57BL/6 mice
2006:Cell culture
1914:Biochemistry
1909:Cell biology
1619:Processivity
1445:synthesis in
1289:
919:Primer-BLAST
896:
869:
863:
853:
841:. Retrieved
831:
819:. Retrieved
809:
795:
752:
748:
700:
696:
650:
644:
611:
607:
597:
578:
521:
520:
508:genetic code
494:, and H for
461:genetic code
448:
446:
427:
423:
415:
395:
387:
380:
373:
366:
333:
246:
218:
195:
183:
145:on both the
140:
131:a strand of
129:synthesizing
122:
107:
106:RNA primers
84:biochemistry
79:the template
62:
51:nucleic acid
46:
44:
2138:WikiProject
1947:Engineering
1902:Linked life
1817:Pribnow box
1775:Translation
1638:Termination
1312:Prokaryotic
1304:Replication
980:Prokaryotic
959:prokaryotic
957:(comparing
843:12 February
375:reaction's
276:, known as
259:direction,
202:prokaryotes
159:synthesized
71:nucleotides
18:DNA primers
2176:Categories
2088:Epigenetic
1999:Techniques
1861:Terminator
1844:trp operon
1839:lac operon
1834:gal operon
1650:Telomerase
1624:DNA ligase
1617:Movement:
1441:Eukaryotic
1412:DNA gyrase
1397:DNA ligase
1316:elongation
1047:Eukaryotic
984:initiation
972:Initiation
963:eukaryotic
872:(3): 437.
697:DNA Repair
553:References
484:isoleucine
481:amino acid
473:amino acid
465:degenerate
463:itself is
431:TA cloning
344:hybridizes
242:DNA ligase
214:DNA ligase
206:eukaryotes
125:initiation
2013:(such as
1871:Repressor
1588:DNA clamp
1402:DNA clamp
1392:Replisome
888:2073-4441
769:1943-0264
719:1568-7864
703:: 28β38.
669:cite book
628:0264-6021
510:for each
457:organisms
355:and the β
59:synthetic
2020:Methods
1954:Concepts
1934:Genetics
1888:Silencer
1866:Enhancer
1822:TATA box
1812:Promoter
1803:Heredity
1739:Overview
1730:Glossary
1646:Telomere
1262:Replicon
1218:Helicase
1209:RNASEH2A
1053:G1 phase
1007:Helicase
821:13 March
787:23378587
727:26303841
636:22849643
540:See also
504:cytosine
490:, T for
419:DECIPHER
357:Next-Gen
302:ligation
274:helicase
169:. Since
137:primases
92:in vitro
2166:Biology
2093:Genetic
2040:Pigment
2029:Protein
1990:Wet lab
1986:Dry lab
1966:Mitosis
1798:Genetic
1789:Element
1779:protein
1720:History
1559:epsilon
1447:S phase
1274:Lagging
1229:Primase
1204:RNASEH1
1199:RNase H
1031:Primase
914:Primer3
778:3552508
534:GenBank
500:thymine
496:adenine
492:thymine
488:adenine
298:ligase1
179:primase
147:leading
142:de novo
108:in vivo
73:to the
2152:Portal
2053:-omics
2042:&
1851:Intron
1829:Operon
1290:Primer
886:
785:
775:
767:
725:
717:
657:
634:
626:
585:
469:codons
340:anneal
75:3β-end
47:primer
32:Primer
1725:Index
1579:POLE4
1574:POLE3
1569:POLE2
1552:POLD4
1547:POLD3
1542:POLD2
1537:POLD1
1532:delta
1525:PRIM2
1520:PRIM1
1515:POLA2
1510:POLA1
1505:alpha
1238:PRIM2
1233:PRIM1
1190:SSBP4
1185:SSBP3
1180:SSBP2
865:Water
512:codon
502:, or
399:BLAST
270:RNase
257:5β²β3β²
233:5β²β3β²
63:oligo
1856:Exon
1665:DKC1
1660:TERC
1655:TERT
1611:Both
1593:PCNA
1564:POLE
1490:RPA1
1473:FEN1
1461:RFC1
1385:holE
1380:holD
1375:holC
1370:holB
1365:holA
1360:dnaX
1355:dnaT
1350:dnaQ
1345:dnaN
1340:dnaH
1335:dnaE
1330:dnaC
1276:and
1247:Both
1222:HFM1
1152:MCM7
1147:MCM6
1142:MCM5
1137:MCM4
1132:MCM3
1127:MCM2
1115:Cdt1
1108:Cdc6
1099:ORC6
1094:ORC5
1089:ORC4
1084:ORC3
1079:ORC2
1074:ORC1
1036:dnaG
1017:dnaB
1012:dnaA
1000:dnaC
884:ISSN
845:2014
823:2012
783:PMID
765:ISSN
723:PMID
715:ISSN
675:link
655:ISBN
632:PMID
624:ISSN
583:ISBN
453:gene
403:NCBI
367:The
278:Pif1
204:and
149:and
117:and
98:and
86:and
57:. A
1769:RNA
1759:DNA
1258:Ori
961:to
874:doi
773:PMC
757:doi
705:doi
616:doi
612:447
318:PCR
255:in
133:DNA
127:of
2178::
2055:")
2038:,
1988:/
1648::
1423::
1231::
1220::
1022:T7
882:.
870:14
868:.
862:.
781:.
771:.
763:.
751:.
747:.
735:^
721:.
713:.
701:34
699:.
695:.
683:^
671:}}
667:{{
630:.
622:.
610:.
606:.
561:^
498:,
304:.
244:.
45:A
2154::
2017:)
1781:)
1777:(
1771:)
1767:(
1761:)
1757:(
1701:e
1694:t
1687:v
1501::
1449:)
1443:(
1318:)
1314:(
1260:/
1256:/
1055:)
1049:(
986:)
982:(
965:)
947:e
940:t
933:v
890:.
876::
847:.
825:.
803:.
789:.
759::
753:5
729:.
707::
677:)
663:.
638:.
618::
591:.
391:m
388:T
384:m
381:T
331:.
34:.
20:)
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