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“Effect of mutations in a simian virus 40 PolyA signal enhancer on green fluorescent protein reporter gene expression”, vol. 10, pp. 1866-1883, 2011.
, Cai L, Fritz D, Stefanovic L and Stefanovic B (2010). Binding of LARP6 to the conserved 5' stem-loop regulates translation of mRNAs encoding type I collagen. J. Mol. Biol. 395: 309-326.
http://dx.doi.org/10.1016/j.jmb.2009.11.020
PMid:19917293 PMCid:2826804
Chou SH, Tseng YY and Chu BY (1999). Stable formation of a pyrimidine-rich loop hairpin in a cruciform promoter. J. Mol. Biol. 292: 309-320.
http://dx.doi.org/10.1006/jmbi.1999.3066
PMid:10493877
Costa FF (2008). Non-coding RNAs, epigenetics and complexity. Gene 410: 9-17.
http://dx.doi.org/10.1016/j.gene.2007.12.008
PMid:18226475
Costantini M and Bernardi G (2008). Correlations between coding and contiguous non-coding sequences in isochore families from vertebrate genomes. Gene 410: 241-248.
http://dx.doi.org/10.1016/j.gene.2007.12.016
PMid:18252269
Dai X, Kloster M and Rothman-Denes LB (1998). Sequence-dependent extrusion of a small DNA hairpin at the N4 virion RNA polymerase promoters. J. Mol. Biol. 283: 43-58.
http://dx.doi.org/10.1006/jmbi.1998.2096
PMid:9761672
Darlow JM and Leach DR (1998). Evidence for two preferred hairpin folding patterns in d(CGG).d(CCG) repeat tracts in vivo. J. Mol. Biol. 275: 17-23.
http://dx.doi.org/10.1006/jmbi.1997.1452
PMid:9451435
Frolov I, Hardy R and Rice CM (2001). Cis-acting RNA elements at the 5' end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis. RNA 7: 1638-1651.
http://dx.doi.org/10.1017/S135583820101010X
PMid:11720292 PMCid:1370205
Gleghorn ML, Davydova EK, Rothman-Denes LB and Murakami KS (2008). Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase. Mol. Cell 32: 707-717.
http://dx.doi.org/10.1016/j.molcel.2008.11.010
PMid:19061645 PMCid:2639713
Grimwood J, Gordon LA, Olsen A, Terry A, et al. (2004). The DNA sequence and biology of human chromosome 19. Nature 428: 529-535.
http://dx.doi.org/10.1038/nature02399
PMid:15057824
Kang H, Feng M, Schroeder ME, Giedroc DP, et al. (2006). Putative cis-acting stem-loops in the 5' untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts. J. Virol. 80: 10600-10614.
http://dx.doi.org/10.1128/JVI.00455-06
PMid:16920822 PMCid:1641749
Kuznetsov SV, Ren CC, Woodson SA and Ansari A (2008). Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res. 36: 1098-1112.
http://dx.doi.org/10.1093/nar/gkm1083
PMid:18096625 PMCid:2275088
Lander ES, Linton LM, Birren B, Nusbaum C, et al. (2001). Initial sequencing and analysis of the human genome. Nature 409: 860-921.
http://dx.doi.org/10.1038/35057062
PMid:11237011
Li L, Kang H, Liu P, Makkinje N, et al. (2008). Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication. J. Mol. Biol. 377: 790-803.
http://dx.doi.org/10.1016/j.jmb.2008.01.068
PMid:18289557 PMCid:2652258
Li Y, Ho ES, Gunderson SI and Kiledjian M (2009). Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5'-end stem-loop structures. Nucleic Acids Res. 37: 2227-2237.
http://dx.doi.org/10.1093/nar/gkp087
PMid:19233875 PMCid:2673433
Lu ZJ, Zhai Y, Wang XF and Song SX (2003). DNA sequence composition on human X chromosome differing from that on chromosomes 6,7,8,10,11 and 12. Genet. Sin. 30: 1051-1060.
Nelson MJ and Green BR (2005). Double hairpin elements and tandem repeats in the non-coding region of Adenoides eludens chloroplast gene minicircles. Gene 358: 102-110.
http://dx.doi.org/10.1016/j.gene.2005.05.024
PMid:16043313
Nickens DG and Hardy RW (2008). Structural and functional analyses of stem-loop 1 of the Sindbis virus genome. Virology 370: 158-172.
http://dx.doi.org/10.1016/j.virol.2007.08.006
PMid:17900652
Rosskopf JJ, Upton JH 3rd, Rodarte L, Romero TA, et al. (2010). A 3' terminal stem-loop structure in Nodamura virus RNA2 forms an essential cis-acting signal for RNA replication. Virus Res. 150: 12-21.
http://dx.doi.org/10.1016/j.virusres.2010.02.006
PMid:20176063 PMCid:3017585
Sean P, Nguyen JHC and Semler BL (2009). Altered interactions between stem-loop IV within the 5' noncoding region of coxsackievirus RNA and poly(rC) binding protein 2: effects on IRES-mediated translation and viral infectivity. Virology 389: 45-58.
http://dx.doi.org/10.1016/j.virol.2009.03.012
PMid:19446305 PMCid:2694229
Ueno M, Kodama EN, Shimura K, Sakurai Y, et al. (2009). Synonymous mutations in stem-loop III of Rev responsive elements enhance HIV-1 replication impaired by primary mutations for resistance to enfuvirtide. Antiviral Res. 82: 67-72.
http://dx.doi.org/10.1016/j.antiviral.2009.02.002
PMid:19428597
Wang XF, Wang X, Liu J, Feng J, et al. (2009a). Alu tandem sequences inhibit GFP gene expression by triggering chromatin wrapping. Genes Genom. 31: 209-215.
http://dx.doi.org/10.1007/BF03191192
Wang XF, Jin X, Wang X, Liu J, et al. (2009b). Effects of L1-ORF2 fragments on green fluorescent protein gene expression. Genet. Mol. Biol. 32: 688-696.
http://dx.doi.org/10.1590/S1415-47572009005000068
PMid:21637438 PMCid:3036906
Xu ZL, Mizuguchi H, Ishii-Watabe A, Uchida E, et al. (2001). Optimization of transcriptional regulatory elements for constructing plasmid vectors. Gene 272: 149-156.
http://dx.doi.org/10.1016/S0378-1119(01)00550-9
Yin K, Wang X, Ma H, Xie Y, et al. (2010). Impact of copy number of distinct SV40PolyA segments on expression of a GFP reporter gene. Sci. China Life Sci. 53: 606-612.
http://dx.doi.org/10.1007/s11427-010-0110-8
PMid:20596944
Yu L and Markoff L (2005). The topology of bulges in the long stem of the flavivirus 3'stem-loop is a major determinant of RNA replication competence. J. Virol. 79: 2309-2324.
http://dx.doi.org/10.1128/JVI.79.4.2309-2324.2005
PMid:15681432 PMCid:546603