Enhanced protocol for determining the 3' terminus of hepatitis C virus.
The determination of viral 3' ends is a routine practice in molecular biology. However, this has been a challenging task for hepatitis C virus (HCV), an enveloped single-stranded, positive-sense RNA virus classified into the Flaviviridae family. The extreme end of HCV 3' untranslated region (3'UTR), the so-called 3' X tail, was not identified at the time of HCV discovery. Complete HCV 3'UTR sequences occupy a very small percentage of the exponentially growing HCV sequence databases. Although commercial kits and experimental protocols are available, these methods are both tedious and not reproducible. A stepwise optimization procedure was developed as a simple and robust protocol for determining the complete HCV 3'UTR from clinical samples. The availability of abundant authentic sequence information for the complete HCV 3'UTR will allow full investigation of its biological role in the life cycle of HCV.
Zhang
Xiaoan
X
Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63110, USA.
Fan
Xiaofeng
X
Xu
Yanjuan
Y
Di Bisceglie
Adrian M
AM
D020413:3' Untranslated Regions; D017931:DNA Primers / Q000235:genetics; D016174:Hepacivirus / Q000235:genetics*; D006801:Humans; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D014773:Virology / Q000379:methods*
D020413:3' Untranslated Regions; D017931:DNA Primers; D012367:RNA, Viral
Biotechniques. 2001 Dec;31(6):1286, 1288, 1290, passim
11768657
J Gen Virol. 2004 Oct;85(Pt 10):3037-3047
15448367
Methods Mol Biol. 2009;510:305-27
19009271
J Clin Virol. 2003 Jul;27(2):152-61
12829037
Biochem Biophys Res Commun. 2007 Nov 9;363(1):171-7
17854768
Nucleic Acids Res. 1999 Mar 15;27(6):1558-60
10037822
RNA. 2004 Sep;10(9):1337-51
15273323
J Mol Biol. 2001 Sep 14;312(2):323-33
11554789
J Virol. 2005 Mar;79(5):3071-83
15709027
Gene. 1988 Dec 15;73(1):237-44
3243435
RNA. 2002 Jun;8(6):824-41
12088154
J Virol. 1996 May;70(5):3307-12
8627816
Nucleic Acids Res. 1992 Aug 25;20(16):4371
1508731
Nucleic Acids Res. 1997 Oct 1;25(19):3957-8
9380524
Trends Biochem Sci. 1997 Jun;22(6):225-6
9204710
Nucleic Acids Res. 2007 Jan;35(Database issue):D363-6
17142229
Anal Biochem. 2002 Feb 15;301(2):168-74
11814287
Biochem Biophys Res Commun. 2006 Aug 11;346(4):1163-72
16793008
Brief Bioinform. 2004 Jun;5(2):150-63
15260895
Science. 1997 Jul 25;277(5325):570-4
9228008
J Virol. 2006 May;80(9):4336-43
16611892
Science. 1989 Apr 21;244(4902):359-62
2523562
J Virol. 1996 Jun;70(6):3363-71
8648666
N Engl J Med. 1999 Aug 19;341(8):556-62
10451460
Bioinformatics. 2005 Feb 1;21(3):379-84
15377502